splitter Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Split sequence(s) into smaller sequences Description splitter splits one or more input sequences into smaller, optionally overlapping, subsequences. The subsequence size and overlap (if any) may be specified. Optionally, feature information will be used. Usage Here is a sample session with splitter Split a sequence into sub-sequences of 10,000 bases (the default size) with no overlap between the sub-sequences: % splitter tembl:BA000025 ba000025.split Split sequence(s) into smaller sequences Go to the input files for this example Go to the output files for this example Example 2 Split a sequence into sub-sequences of 50,000 bases with an overlap of 3,000 bases on each sub-sequence: % splitter tembl:BA000025 ba000025.split -size=50000 -over=3000 Split sequence(s) into smaller sequences Go to the output files for this example Command line arguments Split sequence(s) into smaller sequences Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqall Sequence(s) filename and optional format, or reference (input USA) [-outseq] seqoutall [.] Sequence set(s) filename and optional format (output USA) Additional (Optional) qualifiers: -size integer [10000] Size to split at (Integer 1 or more) -overlap integer [0] Overlap between split sequences (Integer 0 or more) Advanced (Unprompted) qualifiers: -feature boolean [N] Use feature information -addoverlap boolean [N] Include overlap in output sequence size Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outseq" associated qualifiers -osformat2 string Output seq format -osextension2 string File name extension -osname2 string Base file name -osdirectory2 string Output directory -osdbname2 string Database name to add -ossingle2 boolean Separate file for each entry -oufo2 string UFO features -offormat2 string Features format -ofname2 string Features file name -ofdirectory2 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Data files None. Notes Splitting a large sequence into smaller sub-sequences for analysis might be useful in cases where a particularly memory or CPU intensive application will not run quickly enough or at all on the full sequence. This should seldom be necessary in EMBOSS. By default, splitter will write all the sub-sequences to a single file. In some cases, particularly where non-EMBOSS programs are used, it is necessary to have a single sequence per file. To write the sub-sequences into separate files use the command-line switch -ossingle. References None Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0 Known bugs None. See also Program name Description aligncopy Reads and writes alignments aligncopypair Reads and writes pairs from alignments biosed Replace or delete sequence sections codcopy Copy and reformat a codon usage table cutseq Removes a section from a sequence degapseq Removes non-alphabetic (e.g. gap) characters from sequences descseq Alter the name or description of a sequence entret Retrieves sequence entries from flatfile databases and files extractalign Extract regions from a sequence alignment extractfeat Extract features from sequence(s) extractseq Extract regions from a sequence featcopy Reads and writes a feature table featreport Reads and writes a feature table feattext Return a feature table original text listor Write a list file of the logical OR of two sets of sequences makenucseq Create random nucleotide sequences makeprotseq Create random protein sequences maskambignuc Masks all ambiguity characters in nucleotide sequences with N maskambigprot Masks all ambiguity characters in protein sequences with X maskfeat Write a sequence with masked features maskseq Write a sequence with masked regions newseq Create a sequence file from a typed-in sequence nohtml Remove mark-up (e.g. HTML tags) from an ASCII text file noreturn Remove carriage return from ASCII files nospace Remove whitespace from an ASCII text file notab Replace tabs with spaces in an ASCII text file notseq Write to file a subset of an input stream of sequences nthseq Write to file a single sequence from an input stream of sequences nthseqset Reads and writes (returns) one set of sequences from many pasteseq Insert one sequence into another revseq Reverse and complement a nucleotide sequence seqcount Reads and counts sequences seqret Reads and writes (returns) sequences seqretsetall Reads and writes (returns) many sets of sequences seqretsplit Reads sequences and writes them to individual files sizeseq Sort sequences by size skipredundant Remove redundant sequences from an input set skipseq Reads and writes (returns) sequences, skipping first few splitsource Split sequence(s) into original source sequences trimest Remove poly-A tails from nucleotide sequences trimseq Remove unwanted characters from start and end of sequence(s) trimspace Remove extra whitespace from an ASCII text file union Concatenate multiple sequences into a single sequence vectorstrip Removes vectors from the ends of nucleotide sequence(s) yank Add a sequence reference (a full USA) to a list file Author(s) Gary Williams formerly at: MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Completed 22 March 1999 Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None