test_SeqIO Testing reading sff format file Roche/E3MFGYR02_random_10_reads.sff ID and Name='E3MFGYR02JWQ7T', Seq='tcagGGTCTACATGTTGGTTAACCCGTACTGATTTGAATT...GGGCTTa', length=265 ID and Name='E3MFGYR02JA6IL', Seq='tcagTTTTTTTTGGAAAGGAAAACGGACGTACTCATAGAT...AAATGcc', length=271 ID and Name='E3MFGYR02JHD4H', Seq='tcagAAAGACAAGTGGTATCAACGCAGAGTGGCCATTACG...gagaacg', length=310 ... ID and Name='E3MFGYR02F7Z7G', Seq='tcagAATCATCCACTTTTTAACGTTTTGTTTTGTTCATCT...nnnnnnn', length=219 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Checking can write/read as 'fastq-illumina' format Checking can write/read as 'fastq-solexa' format Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Checking can write/read as 'qual' format Checking can write/read as 'sff' format Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading clustal format file Clustalw/cw02.aln ID = 'gi|4959044|gb|AAD34209.1|AF069', Name='', Seq='MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSE...GNRESVV', length=601 ID = 'gi|671626|emb|CAA85685.1|', Name='', Seq='---------MSPQTETKASVGFKAGVKEYKLTYYTPEYET...PAMD---', length=601 Testing reading clustal format file Clustalw/cw02.aln as an alignment M- alignment column 0 E- alignment column 1 N- alignment column 2 S- alignment column 3 D- alignment column 4 || ... V- alignment column 600 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|671626|emb|CAA85685.1|' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading clustal format file Clustalw/opuntia.aln ID = 'gi|6273285|gb|AF191659.1|AF191', Name='', Seq='TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCG...TACCAGA', length=156 ID = 'gi|6273284|gb|AF191658.1|AF191', Name='', Seq='TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCG...TACCAGA', length=156 ID = 'gi|6273287|gb|AF191661.1|AF191', Name='', Seq='TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCG...TACCAGA', length=156 ... ID = 'gi|6273291|gb|AF191665.1|AF191', Name='', Seq='TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCG...TACCAGA', length=156 Testing reading clustal format file Clustalw/opuntia.aln as an alignment TTTTTTT alignment column 0 AAAAAAA alignment column 1 TTTTTTT alignment column 2 AAAAAAA alignment column 3 CCCCCCC alignment column 4 ||||||| ... AAAAAAA alignment column 155 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|6273291|gb|AF191665.1|AF191). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|6273291|gb|AF191665.1|AF191). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|6273291|gb|AF191665.1|AF191). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|6273291|gb|AF191665.1|AF191' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|6273291|gb|AF191665.1|AF191). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|6273291|gb|AF191665.1|AF191). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading clustal format file Clustalw/hedgehog.aln ID = 'gi|167877390|gb|EDS40773.1|', Name='', Seq='MFNLVSGTGGSSCCHRRNCFANRKKFFTMLLIFLLYMVSQ...-------', length=447 ID = 'gi|167234445|ref|NP_001107837.', Name='', Seq='---------------------MRSASAAALLLAALLVVQA...-------', length=447 ID = 'gi|74100009|gb|AAZ99217.1|', Name='', Seq='-------------MPQR----SLRHQLGMILVFFLLVTSH...D------', length=447 ... ID = 'gi|56122354|gb|AAV74328.1|', Name='', Seq='----------------------LAADDQGRLLYSDFLTFL...GMAVKSS', length=447 Testing reading clustal format file Clustalw/hedgehog.aln as an alignment M---- alignment column 0 F---- alignment column 1 N---- alignment column 2 L---- alignment column 3 V---- alignment column 4 ||||| ... ---SS alignment column 446 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|56122354|gb|AAV74328.1|). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|56122354|gb|AAV74328.1|). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|56122354|gb|AAV74328.1|). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|56122354|gb|AAV74328.1|' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|56122354|gb|AAV74328.1|). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|56122354|gb|AAV74328.1|). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading clustal format file Clustalw/odd_consensus.aln ID = 'AT3G20900.1-CDS', Name='', Seq='----------------------------------------...AGAGTAG', length=687 ID = 'AT3G20900.1-SEQ', Name='', Seq='ATGAACAAAGTAGCGAGGAAGAACAAAACATCAGGTGAAC...AGAGTAG', length=687 Testing reading clustal format file Clustalw/odd_consensus.aln as an alignment -A alignment column 0 -T alignment column 1 -G alignment column 2 -A alignment column 3 -A alignment column 4 || ... GG alignment column 686 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Failed: Repeated identifier, possibly due to truncation Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AT3G20900.1-SEQ). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AT3G20900.1-SEQ). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AT3G20900.1-SEQ). Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AT3G20900.1-SEQ). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AT3G20900.1-SEQ). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fasta format file Fasta/lupine.nu ID and Name='gi|5049839|gb|AI730987.1|AI730987', Seq='GAAAATTCATTTTCTTTGGACTTTCTCTGAAATCCGAGTC...GGTTTTT', length=655 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5049839|gb|AI730987.1|AI730987). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5049839|gb|AI730987.1|AI730987). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5049839|gb|AI730987.1|AI730987). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|5049839|gb|AI730987.1|AI730987' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5049839|gb|AI730987.1|AI730987). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5049839|gb|AI730987.1|AI730987). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fasta format file Fasta/elderberry.nu ID and Name='gi|4218935|gb|AF074388.1|AF074388', Seq='ATGAAGTTAAGCACTCTTCTCATCTTATCTTTTCCTTTCC...GTCGTTT', length=2050 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4218935|gb|AF074388.1|AF074388). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4218935|gb|AF074388.1|AF074388). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4218935|gb|AF074388.1|AF074388). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|4218935|gb|AF074388.1|AF074388' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4218935|gb|AF074388.1|AF074388). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4218935|gb|AF074388.1|AF074388). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fasta format file Fasta/phlox.nu ID and Name='gi|5052071|gb|AF067555.1|AF067555', Seq='TCGAAACCTGCCTAGCAGAACGACCCGCGAACTTGTATTC...CACGACC', length=623 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5052071|gb|AF067555.1|AF067555). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5052071|gb|AF067555.1|AF067555). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5052071|gb|AF067555.1|AF067555). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|5052071|gb|AF067555.1|AF067555' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5052071|gb|AF067555.1|AF067555). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5052071|gb|AF067555.1|AF067555). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fasta format file Fasta/centaurea.nu ID and Name='gi|4104054|gb|AH007193.1|SEG_CVIGS', Seq='CCTGTCACTTAACTTTTTGTTCATAAGGTATATATGGGGG...GTTAGAG', length=1002 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4104054|gb|AH007193.1|SEG_CVIGS). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4104054|gb|AH007193.1|SEG_CVIGS). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4104054|gb|AH007193.1|SEG_CVIGS). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|4104054|gb|AH007193.1|SEG_CVIGS' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4104054|gb|AH007193.1|SEG_CVIGS). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4104054|gb|AH007193.1|SEG_CVIGS). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fasta format file Fasta/wisteria.nu ID and Name='gi|5817701|gb|AF142731.1|AF142731', Seq='GCTCCATTTTTTACACATTTCTATGAACTAATTGGTTCAT...ATGATGA', length=2551 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5817701|gb|AF142731.1|AF142731). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5817701|gb|AF142731.1|AF142731). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5817701|gb|AF142731.1|AF142731). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|5817701|gb|AF142731.1|AF142731' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5817701|gb|AF142731.1|AF142731). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5817701|gb|AF142731.1|AF142731). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fasta format file Fasta/sweetpea.nu ID and Name='gi|3176602|gb|U78617.1|LOU78617', Seq='CAGGCTGCGCGGTTTCTATTTATGAAGAACAAGGTCCGTA...GTTTGTT', length=309 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3176602|gb|U78617.1|LOU78617). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3176602|gb|U78617.1|LOU78617). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3176602|gb|U78617.1|LOU78617). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|3176602|gb|U78617.1|LOU78617' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3176602|gb|U78617.1|LOU78617). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3176602|gb|U78617.1|LOU78617). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fasta format file Fasta/lavender.nu ID and Name='gi|5690369|gb|AF158246.1|AF158246', Seq='GGCTCTTAAGTCATGTCTAGGCAGGTGTGCACAAGTTTAG...GTAGGTG', length=550 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5690369|gb|AF158246.1|AF158246). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5690369|gb|AF158246.1|AF158246). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5690369|gb|AF158246.1|AF158246). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|5690369|gb|AF158246.1|AF158246' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5690369|gb|AF158246.1|AF158246). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|5690369|gb|AF158246.1|AF158246). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fasta format file Fasta/aster.pro ID and Name='gi|3298468|dbj|BAA31520.1|', Seq='GGHVNPAVTFGAFVGGNITLLRGIVYIIAQLLGSTVACLL...FIVGANI', length=107 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3298468|dbj|BAA31520.1|). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3298468|dbj|BAA31520.1|). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3298468|dbj|BAA31520.1|). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|3298468|dbj|BAA31520.1|' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3298468|dbj|BAA31520.1|). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3298468|dbj|BAA31520.1|). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fasta format file Fasta/loveliesbleeding.pro ID and Name='gi|2781234|pdb|1JLY|B', Seq='XAGLPVIMCLKSNNHQKYLRYQSDNIQQYGLLQFSADKIL...IELGQNN', length=304 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|2781234|pdb|1JLY|B). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|2781234|pdb|1JLY|B). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|2781234|pdb|1JLY|B). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|2781234|pdb|1JLY|B' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|2781234|pdb|1JLY|B). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|2781234|pdb|1JLY|B). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fasta format file Fasta/rose.pro ID and Name='gi|4959044|gb|AAD34209.1|AF069992_1', Seq='MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSE...GNRESVV', length=600 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4959044|gb|AAD34209.1|AF069992_1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4959044|gb|AAD34209.1|AF069992_1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4959044|gb|AAD34209.1|AF069992_1). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|4959044|gb|AAD34209.1|AF069992_1' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4959044|gb|AAD34209.1|AF069992_1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|4959044|gb|AAD34209.1|AF069992_1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fasta format file Fasta/rosemary.pro ID and Name='gi|671626|emb|CAA85685.1|', Seq='MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAF...FEFPAMD', length=473 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|671626|emb|CAA85685.1|' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|671626|emb|CAA85685.1|). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fasta format file Fasta/f001 ID and Name='gi|3318709|pdb|1A91|', Seq='MENLNMDLLYMAAAVMMGLAAIGAAIGIGILGGKFLEGAA...YVMFAVA', length=79 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3318709|pdb|1A91|). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3318709|pdb|1A91|). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3318709|pdb|1A91|). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|3318709|pdb|1A91|' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3318709|pdb|1A91|). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|3318709|pdb|1A91|). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fasta format file Fasta/f002 ID and Name='gi|1348912|gb|G26680|G26680', Seq='CGGACCAGACGGACACAGGGAGAAGCTAGTTTCTTTCATG...GGTTTNA', length=633 ID and Name='gi|1348917|gb|G26685|G26685', Seq='CGGAGCCAGCGAGCATATGCTGCATGAGGACCTTTCTATC...NNNGAAA', length=413 ID and Name='gi|1592936|gb|G29385|G29385', Seq='GATCAAATCTGCACTGTGTCTACATATAGGAAAGGTCCTG...NTTTTTT', length=471 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|1592936|gb|G29385|G29385). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|1592936|gb|G29385|G29385). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|1592936|gb|G29385|G29385). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|1592936|gb|G29385|G29385' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|1592936|gb|G29385|G29385). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|1592936|gb|G29385|G29385). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading fasta format file Fasta/fa01 ID and Name='AK1H_ECOLI/1-378', Seq='CPDSINAALICRGEKMSIAIMAGVLEARGH-N--VTVIDP...INIVAIA', length=378 ID and Name='AKH_HAEIN/1-382', Seq='-----------------VEDAVKATIDCRGEKLSIAMMKA...SALAQAN', length=382 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AKH_HAEIN/1-382). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AKH_HAEIN/1-382). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AKH_HAEIN/1-382). Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AKH_HAEIN/1-382). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AKH_HAEIN/1-382). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading fasta format file GenBank/NC_005816.fna ID and Name='gi|45478711|ref|NC_005816.1|', Seq='TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTG...ACCCCTG', length=9609 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478711|ref|NC_005816.1|). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478711|ref|NC_005816.1|). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478711|ref|NC_005816.1|). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|45478711|ref|NC_005816.1|' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478711|ref|NC_005816.1|). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478711|ref|NC_005816.1|). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fasta format file GenBank/NC_005816.ffn ID and Name='ref|NC_005816.1|:87-1109', Seq='ATGGTCACTTTTGAGACAGTTATGGAAATTAAAATCCTGC...GGCGTGA', length=1023 ID and Name='ref|NC_005816.1|:1106-1888', Seq='GTGATGATGGAACTGCAACATCAACGACTGATGGCGCTCG...TGAGTAA', length=783 ID and Name='ref|NC_005816.1|:2925-3119', Seq='GTGAACAAACAACAACAAACTGCGCTGAATATGGCGCGAT...AACATAA', length=195 ... ID and Name='ref|NC_005816.1|:c8360-8088', Seq='TTGGCTGATTTGAAAAAGCTACAGGTTTACGGACCTGAGT...CAAGTAA', length=273 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=ref|NC_005816.1|:c8360-8088). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=ref|NC_005816.1|:c8360-8088). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=ref|NC_005816.1|:c8360-8088). Checking can write/read as 'genbank' format Failed: Locus identifier 'ref|NC_005816.1|:c8360-8088' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=ref|NC_005816.1|:c8360-8088). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=ref|NC_005816.1|:c8360-8088). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading fasta format file GenBank/NC_005816.faa ID and Name='gi|45478712|ref|NP_995567.1|', Seq='MVTFETVMEIKILHKQGMSSRAIARELGISRNTVKRYLQA...SFCRGVA', length=340 ID and Name='gi|45478713|ref|NP_995568.1|', Seq='MMMELQHQRLMALAGQLQLESLISAAPALSQQAVDQEWSY...IAEANPE', length=260 ID and Name='gi|45478714|ref|NP_995569.1|', Seq='MNKQQQTALNMARFIRSQSLILLEKLDALDADEQAAMCER...AESETGT', length=64 ... ID and Name='gi|45478721|ref|NP_995576.1|', Seq='MADLKKLQVYGPELPRPYADTVKGSRYKNMKELRVQFSGR...LNTLESK', length=90 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|45478721|ref|NP_995576.1|' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading fasta format file GenBank/NC_000932.faa ID and Name='gi|7525080|ref|NP_051037.1|', Seq='MPTIKQLIRNTRQPIRNVTKSPALRGCPQRRGTCTRVYTI...YGVKKPK', length=123 ID and Name='gi|7525013|ref|NP_051039.1|', Seq='MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMIPT...EAPSTNG', length=353 ID and Name='gi|126022795|ref|NP_051040.2|', Seq='MDKFQGYLEFDGARQQSFLYPLFFREYIYVLAYDHGLNRL...NDLVNHE', length=504 ... ID and Name='gi|7525099|ref|NP_051123.1|', Seq='MAIHLYKTSTPSTRNGAVDSQVKSNPRNNLICGQHHCGKG...ILRRRSK', length=274 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|7525099|ref|NP_051123.1|). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|7525099|ref|NP_051123.1|). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|7525099|ref|NP_051123.1|). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|7525099|ref|NP_051123.1|' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|7525099|ref|NP_051123.1|). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|7525099|ref|NP_051123.1|). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading tab format file GenBank/NC_005816.tsv ID and Name='gi|45478712|ref|NP_995567.1|', Seq='MVTFETVMEIKILHKQGMSSRAIARELGISRNTVKRYLQA...SFCRGVA', length=340 ID and Name='gi|45478713|ref|NP_995568.1|', Seq='MMMELQHQRLMALAGQLQLESLISAAPALSQQAVDQEWSY...IAEANPE', length=260 ID and Name='gi|45478714|ref|NP_995569.1|', Seq='MNKQQQTALNMARFIRSQSLILLEKLDALDADEQAAMCER...AESETGT', length=64 ... ID and Name='gi|45478721|ref|NP_995576.1|', Seq='MADLKKLQVYGPELPRPYADTVKGSRYKNMKELRVQFSGR...LNTLESK', length=90 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|45478721|ref|NP_995576.1|' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|45478721|ref|NP_995576.1|). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading fasta format file GFF/NC_001802.fna ID and Name='gi|9629357|ref|NC_001802.1|', Seq='GGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTC...GTGCTTC', length=9181 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|NC_001802.1|). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|NC_001802.1|). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|NC_001802.1|). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|9629357|ref|NC_001802.1|' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|NC_001802.1|). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|NC_001802.1|). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fasta format file GFF/NC_001802lc.fna ID and Name='gi|9629357|ref|nc_001802.1|', Seq='ggtctctctggttagaccagatctgagcctgggagctctc...gtgcttc', length=9181 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|nc_001802.1|). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|nc_001802.1|). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|nc_001802.1|). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|9629357|ref|nc_001802.1|' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|nc_001802.1|). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|9629357|ref|nc_001802.1|). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fasta format file GFF/multi.fna ID and Name='test1', Seq='ACGTCGCG', length=8 ID and Name='test2', Seq='GGGGCCCC', length=8 ID and Name='test3', Seq='AAACACAC', length=8 Testing reading fasta format file GFF/multi.fna as an alignment AGA alignment column 0 CGA alignment column 1 GGA alignment column 2 TGC alignment column 3 CCA alignment column 4 ||| ... GCC alignment column 7 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=test3). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=test3). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=test3). Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=test3). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=test3). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fasta format file Registry/seqs.fasta ID and Name='gi|1348916|gb|G26684|G26684', Seq='GATCCCTACCCTTNCCGTTGGTCTCTNTCGCTGACTCGAG...TTATTTC', length=285 ID and Name='gi|129628|sp|P07175|PARA_AGRTU', Seq='MPVVVVASSKGGAGKSTTAVVLGTELAHKGVPVTMLDCDP...KLTEALR', length=222 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|129628|sp|P07175|PARA_AGRTU). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|129628|sp|P07175|PARA_AGRTU). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|129628|sp|P07175|PARA_AGRTU). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|129628|sp|P07175|PARA_AGRTU' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|129628|sp|P07175|PARA_AGRTU). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|129628|sp|P07175|PARA_AGRTU). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading nexus format file Nexus/test_Nexus_input.nex ID and Name='t1', Seq='A-C-G-Tc-gtgtgtgctct-t-t------ac-gtgtgtgctct-t-t', length=48 ID and Name='t2 the name', Seq='A-C-GcTc-gtg-----tct-t-t----acac-gtg-----tct-t-t', length=48 ID and Name='isn'that [a] strange name?', Seq='A-CcGcTc-gtgtgtgct--------acacac-gtgtgtgct------', length=48 ... ID and Name='t9', Seq='cccccccc-cccccccccccNc-ccccccccc-cccccccccccNc-c', length=48 Testing reading nexus format file Nexus/test_Nexus_input.nex as an alignment AAAAAAAAc alignment column 0 -----c?tc alignment column 1 CCCCCCCCc alignment column 2 --c-?a-tc alignment column 3 GGGGGGGGc alignment column 4 ||||||||| ... tt--?ag?c alignment column 47 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Cannot have spaces in EMBL accession, 'one should be punished, for (that)!' Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=t9). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=t9). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=t9). Checking can write/read as 'genbank' format Failed: Locus identifier 'one should be punished, for (that)!' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=t9). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=t9). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading swiss format file SwissProt/sp001 ID = 'Q13454', Name='N33_HUMAN', Seq='MGARGAPSRRRQAGRRLRYLPTGSFPFLLLLLLLCIQLGG...YSDLDFE', length=348 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13454). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13454). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13454). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13454). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13454). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading swiss format file SwissProt/sp002 ID = 'P54101', Name='CSP_MOUSE', Seq='MADQRQRSLSTSGESLYHVLGLDKNATSDDIKKSYRKLAL...YHTDGFN', length=198 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P54101). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P54101). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P54101). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P54101). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P54101). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading swiss format file SwissProt/sp003 ID = 'P42655', Name='143E_HUMAN', Seq='MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVE...DVEDENQ', length=255 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P42655). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P42655). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P42655). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P42655). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P42655). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading swiss format file SwissProt/sp004 ID = 'P23082', Name='NDOA_PSEPU', Seq='TVKWIEAVALSDILEGDVLGVTVEGKELALYEVEGEIYAT...RVMIDLS', length=103 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P23082). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P23082). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P23082). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P23082). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P23082). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading swiss format file SwissProt/sp005 ID = 'P24973', Name='NU3M_BALPH', Seq='MNLLLTLLTNTTLALLLVFIAFWLPQLNVYAEKTSPYECG...EGLEWAE', length=115 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P24973). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P24973). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P24973). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P24973). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P24973). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading swiss format file SwissProt/sp006 ID = 'P39896', Name='TCMO_STRGA', Seq='MTPHTHVRGPGDILQLTMAFYGSRALISAVELDLFTLLAG...AIGRKPR', length=339 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P39896). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P39896). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P39896). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P39896). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P39896). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading swiss format file SwissProt/sp007 ID = 'O95832', Name='CLD1_HUMAN', Seq='MANAGLQLLGFILAFLGWIGAIVSTALPQWRIYSYAGDNI...SSGKDYV', length=211 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O95832). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O95832). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O95832). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O95832). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O95832). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading swiss format file SwissProt/sp008 ID = 'P01892', Name='1A02_HUMAN', Seq='MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFFTSVSRPG...SLTACKV', length=365 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01892). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01892). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01892). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01892). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01892). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading swiss format file SwissProt/sp009 ID = 'O23729', Name='CHS3_BROFI', Seq='MAPAMEEIRQAQRAEGPAAVLAIGTSTPPNALYQADYPDY...VPIAGAE', length=394 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O23729). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O23729). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O23729). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O23729). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O23729). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading swiss format file SwissProt/sp010 ID = 'Q13639', Name='5H4_HUMAN', Seq='MDKLDANVSSEEGFGSVEKVVLLTFLSTVILMAILGNLLV...AAQPSDT', length=388 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading swiss format file SwissProt/sp011 ID = 'P16235', Name='LSHR_RAT', Seq='MGRRVPALRQLLVLAVLLLKPSQLQSRELSGSRCPEPCDC...PPRALTH', length=700 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P16235). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P16235). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P16235). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P16235). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P16235). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading swiss format file SwissProt/sp012 ID and Name='Q9Y736', Seq='MQIFVKTLTGKTITLEVESSDTIDNVKTKIQDKEGIPPDQ...LRLRGGN', length=153 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q9Y736). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q9Y736). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q9Y736). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q9Y736). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q9Y736). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading swiss format file SwissProt/sp013 ID and Name='P82909', Seq='MGSKMASASRVVQVVKPHTPLIRFPDRRDNPKPNVSEALR...IQRGGPE', length=102 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P82909). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P82909). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P82909). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P82909). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P82909). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading swiss format file SwissProt/sp014 ID = 'P12166', Name='PSBL_ORYSA', Seq='TQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN', length=37 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P12166). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P12166). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P12166). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P12166). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P12166). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading swiss format file SwissProt/sp015 ID = 'IPI00383150', Name='IPI00383150.2', Seq='MSFQAPRRLLELAGQSLLRDQALAISVLDELPRELFPRLF...FIGPTPC', length=457 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IPI00383150). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IPI00383150). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IPI00383150). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IPI00383150). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IPI00383150). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading swiss format file SwissProt/sp016 ID = 'P01100', Name='FOS_HUMAN', Seq='MMFSGFNADYEASSSRCSSASPAGDSLSYYHSPADSFSSM...SPTLLAL', length=380 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01100). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01100). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01100). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01100). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01100). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading swiss format file Registry/EDD_RAT.dat ID = 'Q62671', Name='EDD_RAT', Seq='ARRERMTAREEASLRTLEGRRRATLLSARQGMMSARGDFL...TKNFGFV', length=920 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q62671). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q62671). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q62671). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q62671). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q62671). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading genbank format file GenBank/noref.gb ID = 'NM_006141.1', Name='NM_006141', Seq='GGCAAGATGGCGCCGGTGGGGGTGGAGAAGAAGCTGCTGC...AAAAAAA', length=1622 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NM_006141.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NM_006141.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NM_006141.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NM_006141.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NM_006141.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading genbank format file GenBank/cor6_6.gb ID = 'X55053.1', Name='ATCOR66M', Seq='AACAAAACACACATCAAAAACGATTTTACAAGAAAAAAAT...AAAAAAA', length=513 ID = 'X62281.1', Name='ATKIN2', Seq='ATTTGGCCTATAAATATAAACCCTTAAGCCCACATATCTT...AATTATA', length=880 ID = 'M81224.1', Name='BNAKINI', Seq='AAAAAAACACAACAAAACTCAATAAATAAACAAATGGCAG...AAGCTTC', length=441 ... ID = 'AF297471.1', Name='AF297471', Seq='ATGGCAGACAACAAGCAGAGCTTCCAAGCCGGTCAAGCCG...CAAGTAG', length=497 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AF297471.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AF297471.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AF297471.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AF297471.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AF297471.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading genbank format file GenBank/iro.gb ID = 'AL109817.1', Name='IRO125195', Seq='CACAGGCCCAGAGCCACTCCTGCCTACAGGTTCTGAGGGC...AAAAAAA', length=1326 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL109817.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL109817.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL109817.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL109817.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL109817.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading genbank format file GenBank/pri1.gb ID = 'U05344.1', Name='HUGLUT1', Seq='GATCATGCATGCACTCCAGCCTGGGACAAGAGCGAAACTC...GTTTGCA', length=741 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U05344.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U05344.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U05344.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U05344.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U05344.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading genbank format file GenBank/arab1.gb ID = 'AC007323.5', Name='AC007323', Seq='AAGCTTTGCTACGATCTACATTTGGGAATGTGAGTCTCTT...GAAGCTT', length=86436 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AC007323.5). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AC007323.5). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AC007323.5). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AC007323.5). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AC007323.5). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading genbank format file GenBank/protein_refseq.gb ID = 'NP_034640.1', Name='NP_034640', Seq='MNNRWILHAAFLLCFSTTALSINYKQLQLQERTNIRKCQE...LTRNFQN', length=182 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading genbank format file GenBank/protein_refseq2.gb ID = 'NP_034640.1', Name='NP_034640', Seq='MNNRWILHAAFLLCFSTTALSINYKQLQLQERTNIRKCQE...LTRNFQN', length=182 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading genbank format file GenBank/extra_keywords.gb ID = 'AL138972.1', Name='DMBR25B3', Seq='TCCAGGGGATTCACGCGCAATATGTTTCCCTCGCTCGTCT...TCGATTG', length=154329 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL138972.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL138972.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL138972.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL138972.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL138972.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading genbank format file GenBank/one_of.gb ID = 'U18266.1', Name='HSTMPO1', Seq='GAATTCAGATAGAATGTAGACAAGAGGGATGGTGAGGAAA...CAAAGGC', length=2509 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U18266.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U18266.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U18266.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U18266.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U18266.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading genbank format file GenBank/NT_019265.gb ID = 'NT_019265.6', Name='NT_019265', Seq='NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...NNNNNNN', length=1250660 Checking can write/read as 'embl' format Checking can write/read as 'genbank' format Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NT_019265.6). Testing reading genbank format file GenBank/origin_line.gb ID = 'NC_002678.1', Name='NC_002678', Seq='TTAATTAACTGTCTTCGATTGCGTTTAATTGACGGTTTTC...TCAGCGC', length=180 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_002678.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_002678.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_002678.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_002678.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_002678.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading genbank format file GenBank/blank_seq.gb ID = 'NP_001832.1', Name='NP_001832', Seq='MEECWVTEIANGSKDGLDSNPMKDYMILSGPQKTAVAVLC...DLDLSDC', length=360 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_001832.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_001832.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_001832.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_001832.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_001832.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading genbank format file GenBank/dbsource_wrap.gb ID = 'P01485', Name='SCX3_BUTOC', Seq='VKDGYIVDDRNCTYFCGRNAYCNEECTKLKGESGYCQWAS...KGPGRCN', length=64 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01485). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01485). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01485). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01485). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01485). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading genbank format file GenBank/NC_005816.gb ID = 'NC_005816.1', Name='NC_005816', Seq='TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTG...ACCCCTG', length=9609 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_005816.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_005816.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_005816.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_005816.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_005816.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading genbank format file GenBank/NC_000932.gb ID = 'NC_000932.1', Name='NC_000932', Seq='ATGGGCGAACGACGGGAATTGAACCCGCGATGGTGAATTC...GGGCATC', length=154478 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_000932.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_000932.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_000932.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_000932.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_000932.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading genbank format file GenBank/pBAD30.gb ID and Name='pBAD30', Seq='GCTAGCGGAGTGTATACTGGCTTACTATGTTGGCACTGAT...GCCCATG', length=4923 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=pBAD30). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=pBAD30). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=pBAD30). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=pBAD30). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=pBAD30). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading genbank format file GenBank/gbvrl1_start.seq ID = 'AB000048.1', Name='AB000048', Seq='ATGTCTGGCAACCAGTATACTGAGGAAGTTATGGAGGGAG...GGATTAA', length=2007 ID = 'AB000049.1', Name='AB000049', Seq='ATGTCTGGCAACCAGTATACTGAGGAAGTTATGGAGGGAG...GGATTAA', length=2007 ID = 'AB000050.1', Name='AB000050', Seq='ATGAGTGATGGAGCAGTTCAACCAGACGGTGGTCAACCTG...ATATTAA', length=1755 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AB000050.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AB000050.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AB000050.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AB000050.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AB000050.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading genbank format file GFF/NC_001422.gbk ID = 'NC_001422.1', Name='NC_001422', Seq='GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCG...ACCTGCA', length=5386 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_001422.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_001422.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_001422.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_001422.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_001422.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading embl format file EMBL/TRBG361.embl ID = 'X56734.1', Name='X56734', Seq='AAACAAACCAAATATGGATTTTATTGTAGCCATATTTGCT...AAAAAAA', length=1859 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X56734.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X56734.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X56734.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X56734.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X56734.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading embl format file EMBL/DD231055_edited.embl ID = 'DD231055.1', Name='DD231055', Seq='GCCGAGCTGACCCAGTCTCCATCCTCCCTGTCTGCATCTG...TATGAGA', length=315 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading embl format file EMBL/SC10H5.embl ID = 'AL031232', Name='SC10H5', Seq='GATCAGTAGACCCAGCGACAGCAGGGCGGGGCCCAGCAGG...CGAGCAT', length=4870 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL031232). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL031232). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL031232). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL031232). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL031232). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading embl format file EMBL/U87107.embl ID = 'U87107.1', Name='U87107', Seq='CAATTACTGCAATGCCCTCGTAATTAAGTGAATTTACAAT...CATCACC', length=8840 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U87107.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U87107.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U87107.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U87107.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U87107.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading embl format file EMBL/AAA03323.embl ID = 'AAA03323.1', Name='AAA03323', Seq='ATGAAGCTTTTAGTGCGCCTAGCACCGATCCTGCTGCTAG...GGTGTGA', length=1545 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AAA03323.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AAA03323.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AAA03323.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AAA03323.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AAA03323.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading embl format file EMBL/AE017046.embl ID = 'AE017046.1', Name='AE017046', Seq='TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTG...ACCCCTG', length=9609 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE017046.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE017046.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE017046.1). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE017046.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE017046.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading embl format file EMBL/Human_contigs.embl ID = 'AJ229040.1', Name='AJ229040', Seq='NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...NNNNNNN', length=958952 ID = 'AL954800.2', Name='AL954800', Seq='NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...NNNNNNN', length=87191216 Checking can write/read as 'embl' format Checking can write/read as 'genbank' format Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL954800.2). Testing reading embl format file EMBL/A04195.imgt ID and Name='A04195', Seq='GATTGATCAATGCAGGCTGTTATGACTCAGGAATCTGCAC...CACATCA', length=51 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading stockholm format file Stockholm/simple.sth ID and Name='AP001509.1', Seq='UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAU...UUAAUGU', length=104 ID and Name='AE007476.1', Seq='AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-U...GUGAGAU', length=104 Testing reading stockholm format file Stockholm/simple.sth as an alignment UA alignment column 0 UA alignment column 1 AA alignment column 2 AA alignment column 3 UU alignment column 4 || ... UU alignment column 103 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE007476.1). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE007476.1). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE007476.1). Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE007476.1). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE007476.1). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading stockholm format file Stockholm/funny.sth ID = 'O83071/192-246', Name='O83071', Seq='MTCRAQLIAVPRASSLAE--AIACAQKM----RVSRVPVYERS', length=43 ID = 'O83071/259-312', Name='O83071', Seq='MQHVSAPVFVFECTRLAY--VQHKLRAH----SRAVAIVLDEY', length=43 ID = 'O31698/18-71', Name='O31698', Seq='MIEADKVAHVQVGNNLEH--ALLVLTKT----GYTAIPVLDPS', length=43 ... ID = 'O31699/88-139', Name='O31699', Seq='EVMLTDIPRLHINDPIMK--GFGMVINN------GFVCVENDE', length=43 Testing reading stockholm format file Stockholm/funny.sth as an alignment MMMEE alignment column 0 TQIVV alignment column 1 CHEMM alignment column 2 RVALL alignment column 3 ASDTT alignment column 4 ||||| ... SYSEE alignment column 42 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O31699/88-139). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O31699/88-139). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O31699/88-139). Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O31699/88-139). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O31699/88-139). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading phylip format file Phylip/reference_dna.phy ID and Name='Archaeopt', Seq='CGATGCTTACCGC', length=13 ID and Name='Hesperorni', Seq='CGTTACTCGTTGT', length=13 ID and Name='Baluchithe', Seq='TAATGTTAATTGT', length=13 ... ID and Name='B.subtilis', Seq='GGCAGCCAATCAC', length=13 Testing reading phylip format file Phylip/reference_dna.phy as an alignment CCTTCG alignment column 0 GGAAAG alignment column 1 ATAAAC alignment column 2 TTTTAA alignment column 3 GAGGAG alignment column 4 |||||| ... CTTTTC alignment column 12 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis). Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading phylip format file Phylip/reference_dna2.phy ID and Name='Archaeopt', Seq='CGATGCTTACCGCCGATGCTTACCGCCGATGCTTACCGC', length=39 ID and Name='Hesperorni', Seq='CGTTACTCGTTGTCGTTACTCGTTGTCGTTACTCGTTGT', length=39 ID and Name='Baluchithe', Seq='TAATGTTAATTGTTAATGTTAATTGTTAATGTTAATTGT', length=39 ... ID and Name='B.subtilis', Seq='GGCAGCCAATCACGGCAGCCAATCACGGCAGCCAATCAC', length=39 Testing reading phylip format file Phylip/reference_dna2.phy as an alignment CCTTCG alignment column 0 GGAAAG alignment column 1 ATAAAC alignment column 2 TTTTAA alignment column 3 GAGGAG alignment column 4 |||||| ... CTTTTC alignment column 38 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis). Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=B.subtilis). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading phylip format file Phylip/hennigian.phy ID and Name='A', Seq='CACACACAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAA', length=40 ID and Name='B', Seq='CACACAACAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAA', length=40 ID and Name='C', Seq='CACAACAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAA', length=40 ... ID and Name='J', Seq='ACAAAAAAAAACAAAAACACAAAAAAAAAAAAAAAAAAAA', length=40 Testing reading phylip format file Phylip/hennigian.phy as an alignment CCCCCAAAAA alignment column 0 AAAAACCCCC alignment column 1 CCCAAAAAAA alignment column 2 AAACCAAAAA alignment column 3 CCAAAAAAAA alignment column 4 |||||||||| ... AAAAAAAAAA alignment column 39 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J). Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading phylip format file Phylip/horses.phy ID and Name='Mesohippus', Seq='AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA', length=40 ID and Name='Hypohippus', Seq='AAACCCCCCCAAAAAAAAACAAAAAAAAAAAAAAAAAAAA', length=40 ID and Name='Archaeohip', Seq='CAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAA', length=40 ... ID and Name='Pliohippus', Seq='CCCACCCCCCCCCACACCCCAAAAAAAAAAAAAAAAAAAA', length=40 Testing reading phylip format file Phylip/horses.phy as an alignment AACCCCCCCC alignment column 0 AAAACCCCCC alignment column 1 AAAAAAAAAC alignment column 2 ACAAAAAAAA alignment column 3 ACACCCCCCC alignment column 4 |||||||||| ... AAAAAAAAAA alignment column 39 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Pliohippus). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Pliohippus). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Pliohippus). Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Pliohippus). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Pliohippus). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading phylip format file Phylip/random.phy ID and Name='A', Seq='CACACAACCAAACAAACCACAAAAAAAAAAAAAAAAAAAA', length=40 ID and Name='B', Seq='AAACCACACACACAAACCCAAAAAAAAAAAAAAAAAAAAA', length=40 ID and Name='C', Seq='ACAAAACCAAACCACCCACAAAAAAAAAAAAAAAAAAAAA', length=40 ... ID and Name='J', Seq='CCAAAAACACCCAACCCAACAAAAAAAAAAAAAAAAAAAA', length=40 Testing reading phylip format file Phylip/random.phy as an alignment CAAAACAAAC alignment column 0 AACAACCACC alignment column 1 CAAAACAAAA alignment column 2 ACAACACACA alignment column 3 CCAAAACCAA alignment column 4 |||||||||| ... AAAAAAAAAA alignment column 39 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J). Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=J). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading phylip format file Phylip/interlaced.phy ID and Name='CYS1_DICDI', Seq='-----MKVILLFVLAVFTVFVSS---------------RG...STSII--', length=384 ID and Name='ALEU_HORVU', Seq='MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRA...SYPVVAA', length=384 ID and Name='CATH_HUMAN', Seq='------MWATLPLLCAGAWLLGV--------PVCGAAELS...SYPIPLV', length=384 Testing reading phylip format file Phylip/interlaced.phy as an alignment -M- alignment column 0 -A- alignment column 1 -H- alignment column 2 -A- alignment column 3 -R- alignment column 4 ||| ... -AV alignment column 383 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CATH_HUMAN). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CATH_HUMAN). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CATH_HUMAN). Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CATH_HUMAN). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CATH_HUMAN). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading phylip format file Phylip/interlaced2.phy ID and Name='IXI_234', Seq='TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCC...AGDRSHE', length=131 ID and Name='IXI_235', Seq='TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCC...AGDRSHE', length=131 ID and Name='IXI_236', Seq='TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCC...AGDRSHE', length=131 ID and Name='IXI_237', Seq='TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----C...AGDRSHE', length=131 Testing reading phylip format file Phylip/interlaced2.phy as an alignment TTTT alignment column 0 SSSS alignment column 1 PPPP alignment column 2 AAAA alignment column 3 SSSS alignment column 4 |||| ... EEEE alignment column 130 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237). Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading emboss format file Emboss/alignret.txt ID = 'IXI_234', Name='', Seq='TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCC...AGDRSHE', length=131 ID = 'IXI_235', Name='', Seq='TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCC...AGDRSHE', length=131 ID = 'IXI_236', Name='', Seq='TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCC...AGDRSHE', length=131 ID = 'IXI_237', Name='', Seq='TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----C...AGDRSHE', length=131 Testing reading emboss format file Emboss/alignret.txt as an alignment TTTT alignment column 0 SSSS alignment column 1 PPPP alignment column 2 AAAA alignment column 3 SSSS alignment column 4 |||| ... EEEE alignment column 130 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237). Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_237). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading emboss format file Emboss/needle.txt ID = 'ref_rec', Name='', Seq='KILIVDD----QYGIRILLNEVFNKEGYQTFQAANGLQAL...-------', length=124 ID = 'gi|94968718|receiver', Name='', Seq='-VLLADDHALVRRGFRLMLED--DPEIEIVAEAGDGAQAV...RVANGET', length=124 ID = 'ref_rec', Name='', Seq='KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVT...-------', length=119 ... ID = 'gi|94970041|receiver', Name='', Seq='TVLLVEDEEGVRKLVRGILSRQGYHVLEATSGEEALEIVR...AVLQKRQ', length=125 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|94970041|receiver). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|94970041|receiver). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|94970041|receiver). Checking can write/read as 'genbank' format Failed: Locus identifier 'gi|94970041|receiver' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|94970041|receiver). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=gi|94970041|receiver). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading emboss format file Emboss/water.txt ID = 'IXI_234', Name='', Seq='TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCC...AGDRSHE', length=131 ID = 'IXI_235', Name='', Seq='TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCC...AGDRSHE', length=131 Testing reading emboss format file Emboss/water.txt as an alignment TT alignment column 0 SS alignment column 1 PP alignment column 2 AA alignment column 3 SS alignment column 4 || ... EE alignment column 130 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_235). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_235). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_235). Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_235). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IXI_235). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading phd format file Phd/phd1 ID and Name='34_222_(80-A03-19).b.ab1', Seq='ctccgtcggaacatcatcggatcctatcacagagtttttg...aagcgtg', length=876 ID and Name='425_103_(81-A03-19).g.ab1', Seq='cgggatcccacctgatccgaggtcaacctgaaaaaatatg...agccaag', length=862 ID and Name='425_7_(71-A03-19).b.ab1', Seq='acataaatcaaattactnaccaacacacaaaccngtctcg...tgctttn', length=1280 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Checking can write/read as 'fastq-illumina' format UserWarning - Data loss - max PHRED quality 62 in Illumina FASTQ Checking can write/read as 'fastq-solexa' format UserWarning - Data loss - max Solexa quality 62 in Solexa FASTQ Checking can write/read as 'genbank' format Failed: Locus identifier '425_7_(71-A03-19).b.ab1' is too long Checking can write/read as 'phd' format Checking can write/read as 'qual' format Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading phd format file Phd/phd2 ID and Name='ML4924R', Seq='actttggtcgcctgcaggtaccggtccgngattcccgggt...ggtgaga', length=180 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Checking can write/read as 'fastq-illumina' format Checking can write/read as 'fastq-solexa' format Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Checking can write/read as 'qual' format Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading phd format file Phd/phd_solexa ID and Name='HWI-EAS94_4_1_1_537_446', Seq='gccaatcaggtttctctgcaagcccctttagcagctgagc', length=40 ID and Name='HWI-EAS94_4_1_1_602_99', Seq='gccatggcacatatatgaaggtcagaggacaacttgctgt', length=40 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Failed: Repeated identifier, possibly due to truncation Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Checking can write/read as 'fastq-illumina' format Checking can write/read as 'fastq-solexa' format Checking can write/read as 'genbank' format Failed: Locus identifier 'HWI-EAS94_4_1_1_602_99' is too long Checking can write/read as 'phd' format Checking can write/read as 'qual' format Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading phd format file Phd/phd_454 ID and Name='EBE03TV04IHLTF.77-243', Seq='ggggatgaaagggatctcggtggtaggtga', length=30 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Checking can write/read as 'fastq-illumina' format Checking can write/read as 'fastq-solexa' format Checking can write/read as 'genbank' format Failed: Locus identifier 'EBE03TV04IHLTF.77-243' is too long Checking can write/read as 'phd' format Checking can write/read as 'qual' format Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading ace format file Ace/contig1.ace ID and Name='Contig1', Seq='aatacgGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAAC...CTAGtac', length=856 ID and Name='Contig2', Seq='cacggatgatagcttcgcgacactagcttttcagctaacc...cttgtag', length=3296 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Checking can write/read as 'fastq-illumina' format Checking can write/read as 'fastq-solexa' format Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Checking can write/read as 'qual' format Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading ace format file Ace/consed_sample.ace ID and Name='Contig1', Seq='agccccgggccgtggggttccttgagcactcccaaagttc...gggtttg', length=1475 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Checking can write/read as 'fastq-illumina' format Checking can write/read as 'fastq-solexa' format Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Checking can write/read as 'qual' format Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading ace format file Ace/seq.cap.ace ID and Name='Contig1', Seq='AGTTTTAGTTTTCCTCTGAAGCAAGCACACCTTCCCTTTC...TCACATT', length=1222 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format UserWarning - Data loss - max PHRED quality 93 in Sanger FASTQ Checking can write/read as 'fastq-illumina' format Checking can write/read as 'fastq-solexa' format Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Checking can write/read as 'qual' format Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading ig format file IntelliGenetics/TAT_mase_nuc.txt ID and Name='A_U455', Seq='ATGGAGCCAGTAGATCCTAACCTAGAGCCCTGGAAACACC...ATTCGCT', length=303 ID and Name='B_HXB2R', Seq='ATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATC...CGATTAG', length=306 ID and Name='C_UG268A', Seq='%CAGGAAGTCAGCCTAAAACTCCTTGTACTAAGTGTTTTG...AGATTAA', length=267 ... ID and Name='SYK_SYK', Seq='ATGTCCTCAACGGACCAGATATGCCAGACACAGAGGGTAC...GAATCTT', length=330 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK_SYK). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK_SYK). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK_SYK). Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK_SYK). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK_SYK). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading ig format file IntelliGenetics/VIF_mase-pro.txt ID and Name='most-likely', Seq='MEN--RW-QVMIVWQVDRMRIRTWKSLVKHHMYRSKKA-K...-----GH', length=298 ID and Name='U455', Seq='MEN--RW-QVMIVWQVDRMKIRTWNSLVKHHMYVSKKA-Q...-----RH', length=298 ID and Name='HXB2R', Seq='MEN--RW-QVMIVWQVDRMRIRTWKSLVKHHMYVSGKA-R...-----GH', length=298 ... ID and Name='SYK', Seq='MEK--EW-IVVPTWRMTPRQIDRLQHIIKTHKYKSKELEK...-------', length=298 Testing reading ig format file IntelliGenetics/VIF_mase-pro.txt as an alignment MMMMMMMMMMMMMMMM alignment column 0 EEEEEEETEEEENEEE alignment column 1 NNNNNNNAEEEEQRKK alignment column 2 --------DEEEEE-- alignment column 3 --------KKKKKK-- alignment column 4 |||||||||||||||| ... HHHHHHH-AAAAL-R- alignment column 297 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK). Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=SYK). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading ig format file IntelliGenetics/vpu_nucaligned.txt ID and Name='VPU_CONSENSUS', Seq='ATGc?tcattt?ga??t?ttagcaaTaa?agcattaatag...?gA?ctg', length=294 ID and Name='A_U455', Seq='ATGACACCTTTGGAAATCTGGGCAATAACAGGGCTGATAG...-AATTTG', length=294 ID and Name='B_SF2', Seq='ATGCAATCTTTACAAATATTAGCAATAGTATCATTAGTAG...-GATCTG', length=294 ... ID and Name='CPZANT', Seq='ATGACTAATATATTTGAGTATGCTTTT-------------...-GACGAA', length=294 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CPZANT). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CPZANT). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CPZANT). Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CPZANT). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CPZANT). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading pir format file NBRF/B_nuc.pir ID and Name='HLA:HLA00132', Seq='ATGCTGGTCATGGCGCCCCGAACCGTCCTCCTGCTGCTCT...AGCTTGA', length=1089 ID and Name='HLA:HLA00133', Seq='ATGCTGGTCATGGCGCCCCGAACCGTCCTCCTGCTGCTCT...AAGAGTT', length=1009 ID and Name='HLA:HLA00134', Seq='GCTCCCACTCCATGAGGTATTTCTACACCTCCGTGTCCCG...CGCGCTG', length=546 ... ID and Name='HLA:HLA01135', Seq='ATGCGGGTCACGGCGCCCCGAACCCTCCTCCTGCTGCTCT...CGCGCGG', length=619 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01135). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01135). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01135). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01135). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01135). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading pir format file NBRF/Cw_prot.pir ID and Name='HLA:HLA00401', Seq='MRVMAPRTLILLLSGALALTETWACSHSMKYFFTSVSRPG...SLIACKA', length=366 ID and Name='HLA:HLA00402', Seq='MRVMAPRTLILLLSGALALTETWACSHSMKYFFTSVSRPG...SLIACKA', length=366 ID and Name='HLA:HLA01075', Seq='MRVMAPRTLILLLSGALALTETWACSHSMKYFFTSVSRPG...SLIACKA', length=366 ... ID and Name='HLA:HLA00484', Seq='MRVMAPRALLLLLSGGLALTETWACSHSMRYFDTAVSRPG...SLIACKA', length=366 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00484). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00484). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00484). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00484). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00484). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading pir format file NBRF/DMA_nuc.pir ID and Name='HLA:HLA00485', Seq='ATGGGTCATGAACAGAACCAAGGAGCTGCGCTGCTACAGA...TGACTGA', length=786 ID and Name='HLA:HLA00486', Seq='CTCCTACTCCAATGTGGCCAGATGACCTGCAAAACCACAC...TATTGGG', length=564 ID and Name='HLA:HLA00487', Seq='GGGTTTCCTATCGCTGAAGTGTTCACGCTGAAGCCCCTGG...CTATTGG', length=279 ID and Name='HLA:HLA00488', Seq='GGGTTTCCTATCGCTGAAGTGTTCACGCTGAAGCCCCTGG...CTATTGG', length=279 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00488). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00488). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00488). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00488). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00488). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading pir format file NBRF/DMB_prot.pir ID and Name='HLA:HLA00489', Seq='MITFLPLLLGLSLGCTGAGGFVAHVESTCLLDDAGTPKDF...SEGWHIS', length=263 ID and Name='HLA:HLA00490', Seq='PPSVQVAKTTPFNTREPVMLACYVWGFYPAEVTITWRKNG...EPILRDW', length=94 ID and Name='HLA:HLA00491', Seq='PPSVQVAKTTPFNTREPVMLACYVWGFYPAEVTITWRKNG...EPILRDW', length=94 ... ID and Name='HLA:HLA01083', Seq='GFVAHVESTCLLDDAGTPKDFTYCIFFNKDLLTCWDPEEN...EPILRDW', length=188 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01083). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01083). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01083). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01083). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01083). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing reading pir format file NBRF/clustalw.pir ID and Name='804Angiostrongylus_cantonensis', Seq='----------------------------------------...-------', length=2527 ID and Name='815Parelaphostrongylus_odocoil', Seq='----------------------------------------...-------', length=2527 Testing reading pir format file NBRF/clustalw.pir as an alignment -- alignment column 0 -- alignment column 1 -- alignment column 2 -- alignment column 3 -- alignment column 4 || ... -- alignment column 2526 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=815Parelaphostrongylus_odocoil). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=815Parelaphostrongylus_odocoil). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=815Parelaphostrongylus_odocoil). Checking can write/read as 'genbank' format Failed: Locus identifier '815Parelaphostrongylus_odocoil' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=815Parelaphostrongylus_odocoil). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=815Parelaphostrongylus_odocoil). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing reading fasta format file Quality/example.fasta ID and Name='EAS54_6_R1_2_1_413_324', Seq='CCCTTCTTGTCTTCAGCGTTTCTCC', length=25 ID and Name='EAS54_6_R1_2_1_540_792', Seq='TTGGCAGGCCAAGGCCGATGGATCA', length=25 ID and Name='EAS54_6_R1_2_1_443_348', Seq='GTTGCTTCTGGCGTGGGTGGGGGGG', length=25 Testing reading fasta format file Quality/example.fasta as an alignment CTG alignment column 0 CTT alignment column 1 CGT alignment column 2 TGG alignment column 3 TCC alignment column 4 ||| ... CAG alignment column 24 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Failed: Repeated identifier, possibly due to truncation Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=EAS54_6_R1_2_1_443_348). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=EAS54_6_R1_2_1_443_348). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=EAS54_6_R1_2_1_443_348). Checking can write/read as 'genbank' format Failed: Locus identifier 'EAS54_6_R1_2_1_443_348' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=EAS54_6_R1_2_1_443_348). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=EAS54_6_R1_2_1_443_348). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading qual format file Quality/example.qual ID and Name='EAS54_6_R1_2_1_413_324', Seq='?????????????????????????', length=25 ID and Name='EAS54_6_R1_2_1_540_792', Seq='?????????????????????????', length=25 ID and Name='EAS54_6_R1_2_1_443_348', Seq='?????????????????????????', length=25 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Failed: Repeated identifier, possibly due to truncation Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Checking can write/read as 'fastq-illumina' format Checking can write/read as 'fastq-solexa' format Checking can write/read as 'genbank' format Failed: Locus identifier 'EAS54_6_R1_2_1_443_348' is too long Checking can write/read as 'phd' format Checking can write/read as 'qual' format Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fastq format file Quality/example.fastq ID and Name='EAS54_6_R1_2_1_413_324', Seq='CCCTTCTTGTCTTCAGCGTTTCTCC', length=25 ID and Name='EAS54_6_R1_2_1_540_792', Seq='TTGGCAGGCCAAGGCCGATGGATCA', length=25 ID and Name='EAS54_6_R1_2_1_443_348', Seq='GTTGCTTCTGGCGTGGGTGGGGGGG', length=25 Testing reading fastq format file Quality/example.fastq as an alignment CTG alignment column 0 CTT alignment column 1 CGT alignment column 2 TGG alignment column 3 TCC alignment column 4 ||| ... CAG alignment column 24 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Failed: Repeated identifier, possibly due to truncation Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Checking can write/read as 'fastq-illumina' format Checking can write/read as 'fastq-solexa' format Checking can write/read as 'genbank' format Failed: Locus identifier 'EAS54_6_R1_2_1_443_348' is too long Checking can write/read as 'phd' format Checking can write/read as 'qual' format Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fastq format file Quality/tricky.fastq ID and Name='071113_EAS56_0053:1:1:998:236', Seq='TTTCTTGCCCCCATAGACTGAGACCTTCCCTAAATA', length=36 ID and Name='071113_EAS56_0053:1:1:182:712', Seq='ACCCAGCTAATTTTTGTATTTTTGTTAGAGACAGTG', length=36 ID and Name='071113_EAS56_0053:1:1:153:10', Seq='TGTTCTGAAGGAAGGTGTGCGTGCGTGTGTGTGTGT', length=36 ID and Name='071113_EAS56_0053:1:3:990:501', Seq='TGGGAGGTTTTATGTGGAAAGCAGCAATGTACAAGA', length=36 Testing reading fastq format file Quality/tricky.fastq as an alignment TATT alignment column 0 TCGG alignment column 1 TCTG alignment column 2 CCTG alignment column 3 TACA alignment column 4 |||| ... AGTA alignment column 35 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Failed: Repeated identifier, possibly due to truncation Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Checking can write/read as 'fastq-illumina' format Checking can write/read as 'fastq-solexa' format Checking can write/read as 'genbank' format Failed: Locus identifier '071113_EAS56_0053:1:3:990:501' is too long Checking can write/read as 'phd' format Checking can write/read as 'qual' format Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fastq format file Quality/sanger_faked.fastq ID and Name='Test', Seq='ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTN', length=41 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Checking can write/read as 'fastq-illumina' format Checking can write/read as 'fastq-solexa' format Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Checking can write/read as 'qual' format Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fastq format file Quality/sanger_93.fastq ID and Name='Test', Seq='ACTGACTGACTGACTGACTGACTGACTGACTGACTGACTG...GACTGAN', length=94 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Checking can write/read as 'fastq-illumina' format Checking can write/read as 'fastq-solexa' format Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Checking can write/read as 'qual' format Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fastq-illumina format file Quality/illumina_faked.fastq ID and Name='Test', Seq='ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTN', length=41 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Checking can write/read as 'fastq-illumina' format Checking can write/read as 'fastq-solexa' format Checking can write/read as 'genbank' format Failed: Need a Nucleotide or Protein alphabet Checking can write/read as 'phd' format Checking can write/read as 'qual' format Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fastq-solexa format file Quality/solexa_faked.fastq ID and Name='slxa_0001_1_0001_01', Seq='ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN', length=46 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Checking can write/read as 'fastq-illumina' format Checking can write/read as 'fastq-solexa' format Checking can write/read as 'genbank' format Failed: Locus identifier 'slxa_0001_1_0001_01' is too long Checking can write/read as 'phd' format Checking can write/read as 'qual' format Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Testing reading fastq-solexa format file Quality/solexa_example.fastq ID and Name='SLXA-B3_649_FC8437_R1_1_1_610_79', Seq='GATGTGCAATACCTTTGTAGAGGAA', length=25 ID and Name='SLXA-B3_649_FC8437_R1_1_1_397_389', Seq='GGTTTGAGAAAGAGAAATGAGATAA', length=25 ID and Name='SLXA-B3_649_FC8437_R1_1_1_850_123', Seq='GAGGGTGTTGATCATGATGATGGCG', length=25 ... ID and Name='SLXA-B3_649_FC8437_R1_1_1_183_714', Seq='GTATTATTTAATGGCATACACTCAA', length=25 Testing reading fastq-solexa format file Quality/solexa_example.fastq as an alignment GGGGG alignment column 0 AGAGT alignment column 1 TTGAA alignment column 2 GTGAT alignment column 3 TTGAT alignment column 4 ||||| ... AAGGA alignment column 24 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Failed: Repeated identifier, possibly due to truncation Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Checking can write/read as 'fastq-illumina' format Checking can write/read as 'fastq-solexa' format Checking can write/read as 'genbank' format Failed: Locus identifier 'SLXA-B3_649_FC8437_R1_1_1_183_714' is too long Checking can write/read as 'phd' format Checking can write/read as 'qual' format Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet Finished tested reading files Starting testing writing records (Note that some of these are expected to 'fail' and say why) Testing can write/read zero records Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Must have at least one sequence Checking can write/read as 'phylip' format Failed: Must have at least one sequence Checking can write/read as 'stockholm' format Failed: Must have at least one sequence Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Checking can write/read as 'fastq-illumina' format Checking can write/read as 'fastq-solexa' format Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Checking can write/read as 'qual' format Checking can write/read as 'sff' format Failed: Need at least one record for SFF output Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Must have at least one sequence Testing can write/read three peptides of different lengths Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Alpha). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Alpha). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Alpha). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Alpha). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Alpha). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Failed: Sequences must all be the same length Testing can write/read three proteins alignment Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Alpha). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Alpha). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Alpha). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Alpha). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Alpha). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing can write/read three DNA sequence alignment Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing can write/read 3 DNA seq alignment with CR/LF in name/descr Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Checking can write/read as 'embl' format Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X). Checking can write/read as 'genbank' format Failed: Locus identifier 'The\nMystery\rSequece:\r\nX' is too long Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Testing can write/read alignment with repeated record Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Failed: Repeated identifier, possibly due to truncation Checking can write/read as 'stockholm' format Failed: Duplicate record identifier: Beta Checking can write/read as 'embl' format Failed: Need a Nucleotide alphabet Checking can write/read as 'fastq' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Alpha). Checking can write/read as 'fastq-illumina' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Alpha). Checking can write/read as 'fastq-solexa' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Alpha). Checking can write/read as 'genbank' format Checking can write/read as 'phd' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Alpha). Checking can write/read as 'qual' format Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Alpha). Checking can write/read as 'sff' format Failed: Missing SFF flow information Checking can write/read as 'tab' format Checking can write/read as 'nexus' format Writing no records to sff format failed: Need at least one record for SFF output Finished tested writing files