USAGE blast_formatter [-h] [-help] [-rid BLAST_RID] [-archive ArchiveFile] [-outfmt format] [-show_gis] [-num_descriptions int_value] [-num_alignments int_value] [-line_length line_length] [-html] [-sorthits sort_hits] [-sorthsps sort_hsps] [-max_target_seqs num_sequences] [-out output_file] [-parse_deflines] [-version] DESCRIPTION Stand-alone BLAST formatter client, version 2.14.0+ OPTIONAL ARGUMENTS -h Print USAGE and DESCRIPTION; ignore all other parameters -help Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters -version Print version number; ignore other arguments *** Input options -rid BLAST Request ID (RID) * Incompatible with: archive -archive File containing BLAST Archive format in ASN.1 (i.e.: output format 11) * Incompatible with: rid *** Formatting options -outfmt alignment view options: 0 = Pairwise, 1 = Query-anchored showing identities, 2 = Query-anchored no identities, 3 = Flat query-anchored showing identities, 4 = Flat query-anchored no identities, 5 = BLAST XML, 6 = Tabular, 7 = Tabular with comment lines, 8 = Seqalign (Text ASN.1), 9 = Seqalign (Binary ASN.1), 10 = Comma-separated values, 11 = BLAST archive (ASN.1), 12 = Seqalign (JSON), 13 = Multiple-file BLAST JSON, 14 = Multiple-file BLAST XML2, 15 = Single-file BLAST JSON, 16 = Single-file BLAST XML2, 17 = Sequence Alignment/Map (SAM), 18 = Organism Report Options 6, 7, 10 and 17 can be additionally configured to produce a custom format specified by space delimited format specifiers, or in the case of options 6, 7, and 10, by a token specified by the delim keyword. E.g.: "17 delim=@ qacc sacc score". The delim keyword must appear after the numeric output format specification. The supported format specifiers for options 6, 7 and 10 are: qseqid means Query Seq-id qgi means Query GI qacc means Query accesion qaccver means Query accesion.version qlen means Query sequence length sseqid means Subject Seq-id sallseqid means All subject Seq-id(s), separated by a ';' sgi means Subject GI sallgi means All subject GIs sacc means Subject accession saccver means Subject accession.version sallacc means All subject accessions slen means Subject sequence length qstart means Start of alignment in query qend means End of alignment in query sstart means Start of alignment in subject send means End of alignment in subject qseq means Aligned part of query sequence sseq means Aligned part of subject sequence evalue means Expect value bitscore means Bit score score means Raw score length means Alignment length pident means Percentage of identical matches nident means Number of identical matches mismatch means Number of mismatches positive means Number of positive-scoring matches gapopen means Number of gap openings gaps means Total number of gaps ppos means Percentage of positive-scoring matches frames means Query and subject frames separated by a '/' qframe means Query frame sframe means Subject frame btop means Blast traceback operations (BTOP) staxid means Subject Taxonomy ID ssciname means Subject Scientific Name scomname means Subject Common Name sblastname means Subject Blast Name sskingdom means Subject Super Kingdom staxids means unique Subject Taxonomy ID(s), separated by a ';' (in numerical order) sscinames means unique Subject Scientific Name(s), separated by a ';' scomnames means unique Subject Common Name(s), separated by a ';' sblastnames means unique Subject Blast Name(s), separated by a ';' (in alphabetical order) sskingdoms means unique Subject Super Kingdom(s), separated by a ';' (in alphabetical order) stitle means Subject Title salltitles means All Subject Title(s), separated by a '<>' sstrand means Subject Strand qcovs means Query Coverage Per Subject qcovhsp means Query Coverage Per HSP qcovus means Query Coverage Per Unique Subject (blastn only) When not provided, the default value is: 'qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore', which is equivalent to the keyword 'std' The supported format specifier for option 17 is: SQ means Include Sequence Data SR means Subject as Reference Seq Default = `0' -show_gis Show NCBI GIs in deflines? -num_descriptions =0> Number of database sequences to show one-line descriptions for Not applicable for outfmt > 4 Default = `500' * Incompatible with: max_target_seqs -num_alignments =0> Number of database sequences to show alignments for Default = `250' * Incompatible with: max_target_seqs -line_length =1> Line length for formatting alignments Not applicable for outfmt > 4 Default = `60' -html Produce HTML output? -sorthits =0 and =<4)> Sorting option for hits: alignment view options: 0 = Sort by evalue, 1 = Sort by bit score, 2 = Sort by total score, 3 = Sort by percent identity, 4 = Sort by query coverage Not applicable for outfmt > 4 -sorthsps =0 and =<4)> Sorting option for hps: 0 = Sort by hsp evalue, 1 = Sort by hsp score, 2 = Sort by hsp query start, 3 = Sort by hsp percent identity, 4 = Sort by hsp subject start Not applicable for outfmt != 0 *** Restrict search or results -max_target_seqs =1> Maximum number of aligned sequences to keep (value of 5 or more is recommended) Default = `500' * Incompatible with: num_descriptions, num_alignments *** Output configuration options -out Output file name Default = `-' *** Miscellaneous options -parse_deflines Should the query and subject defline(s) be parsed?