                                 seqretsplit



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

   Read sequences and write them to individual files

Description

   seqretsplit is a variant of the standard program for reading and
   writing sequences, seqret. It performs exactly the same function except
   that when it reads more than one sequence, it writes each sequence to
   an individual file. In all other respects, skipseq is the same as
   seqret. Its main use is therefore to split a file containing multiple
   sequences into many files, each containing one sequence. There are many
   options built-in into EMBOSS for detailed specification of the input
   and output sequences, for example the sequence type and file format.
   Optionally, feature information will be read and written.

Usage

   Here is a sample session with seqretsplit


% seqretsplit tembl:m1190*
Read sequences and write them to individual files
output sequence(s) [m11903.fasta]:


   Go to the input files for this example
   Go to the output files for this example

   The specification of the output file is not used in this case.

   At some point this ought to change and you will not be prompted for the
   output file at all.

Command line arguments

Read sequences and write them to individual files
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     (Gapped) sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outseq]            seqoutall  [.] Sequence set(s)
                                  filename and optional format (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -feature            boolean    Use feature information
   -firstonly          boolean    Read one sequence and stop

   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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


Input file format

   seqretsplit reads one or more nucleotide or protein sequences.

   The input is a standard EMBOSS sequence query (also known as a 'USA').

   Major sequence database sources defined as standard in EMBOSS
   installations include srs:embl, srs:uniprot and ensembl

   Data can also be read from sequence output in any supported format
   written by an EMBOSS or third-party application.

   The input format can be specified by using the command-line qualifier
   -sformat xxx, where 'xxx' is replaced by the name of the required
   format. The available format names are: gff (gff3), gff2, embl (em),
   genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
   dasgff and debug.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

  Input files for usage example

   'tembl:m1190*' is a sequence entry in the example nucleic acid database
   'tembl'

Output file format

   The output is a standard EMBOSS sequence file.

   The results can be output in one of several styles by using the
   command-line qualifier -osformat xxx, where 'xxx' is replaced by the
   name of the required format. The available format names are: embl,
   genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq,
   excel, feattable, motif, nametable, regions, seqtable, simple, srs,
   table, tagseq.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

  Output files for usage example

  File: m11903.fasta

>M11903 M11903.1 Rattus norvegicus androgen-responsive protein precursor (Svf) g
ene, exons 1 and 1A, alternatively spliced.
cctttcaaatagaaactctcgtgaaggctgtctgagaacacaagctcaaggttgtgactg
atttcagtgatgccgtcttgaagagggataccgtgctagagaatgactcctgatcaaccc
tgaagacttctgcaagcccgaagtcgtgcttccccactctgaactgacatatgttcagga
agtagagacgtgcaccgttggatgttctcaaggtaaaaaggaagatttggaagaatgctc
tagtgttgttgccttggagaggaccagggaacagtacaagactcctactgagcagagaga
aaggagcctgacatttaccgataagaaaggtcatttgccttccaacctgtaggcaaggcc
agacaaggaaatatataaaggagaacctcagatcagctctcagtcaagacccttcctgac
aagatgagtcccaccgggttcttcctccttacggtgctccttgttctggtgacagaagca
gcctcgagggggccccgaggtgagtggcaattttgtgctatgggaaagatgtttgagaac
tatgttctcaaaagggagtctgcagaatgctgtgttcccagggcttctccatgaaggaaa
cttgagtcttttcaagctttaaccatagtcctactgtgagtctctgtgacttgacaagca
acattgctggtaaggagggctgagggggaatgcgggcaacggcctcgggtaacatcctca
ttgt

  File: m11904.fasta

>M11904 M11904.1 Rattus norvegicus androgen-responsive protein precursor (Svf) g
ene, exon 2 and complete cds.
ggtatctccaaacacagcagctggctctcaacagagagtcctcatgcacaactaatccaa
gatacagaaagtggatatagagaatgagacattgttttctctcaacagaaaaattctcac
agtcagctgaagacccttatagtgaaaacatgaatctaaagattctggcgagcgggaggg
gatcaagttctacctttggggcattcagccgaagtgagaactctcggagtaacttcaaat
caaaaagtccaagcagtatcaccagggagaaagtgaatgaggaaagcaggagtgaaatga
gtagtaccagcagccattttggtctcaaaatgagaagatctcatggaggaggagaaatga
atccctttgaaaccaaagtaaagacccggatcactcgcaaataatgtgttccccggccaa
ctgaagacttgagcccaataggcaggtaagtgttatcaccaggtgagggcttacaaacta
ctcgtgcctaatccctaggccattgtaggattgtgcacgcagtaaagttgctataagggg
aggtatggaaacgacctacaaggcagacaaagatacgagctatactgtgt

  File: m11905.fasta

>M11905 M11905.1 Rattus norvegicus androgen-responsive protein precursor (Svf) g
ene, exon 3.
ccgtgcaatctcttcctgtgtccacacagccctgttagaagcaactctctcgttctcaag
gccctacctgcaagaactacctttctcttcctccgcccaacaaaggaggaatgtttctgc
ttgtgacccaccagagatgaaatatagcagtgtcctgcagtaaaggggggccccagaggc
atgggacatacacgcattaatccctccacgtcttccctgtcctacctcacaggttgtcct
cgttccctgggtgtcactgaactaagagaagtctatgatgtcttcaggatgcaggatccc
acaggtgccccggaaatagtccgtgcttcttatttcctccttacacttgttttctttaag
attccggaacctgacaagattcaaatttaaccttttcaataaaaaagatactattctgca
tcattatctcctgaaatctcttgcttctgcagtacaggggctgggtgggattcctaaact
tgaccagttctgccgttaaaggaagatcccttctgtgccgtatcagagactatttccaga
ctctggataga

   One file for each input sequence is written out.

   The names of the files it creates are derived from the ID name of the
   sequence, followed by an extension denoting the format of the sequence.
   You have no control over the names of the files it writes out.

   For example, if the files embl:hsfa11* are read in and the output is
   specified as wibble.seq, then the following files are expected to be
   created:

hsfa110.fasta
hsfa111.fasta
hsfa112.fasta
hsfa113.fasta
hsfa114.fasta

   (No file wibble.seq is created.)

Data files

   None.

Notes

   See the documentation for seqret to see the full range of things that
   you can do when reading and writing sequences.

   Some non-EMBOSS programs will accept only single sequences. In such
   cases seqretsplit is useful for splitting a multiple sequence file into
   many individual files. Some EMBOSS programs will also read only a
   single sequence, which may, however, be one of many in a file. You can
   specify the sequence using the USA filename:sequenceID. Nonetheless,
   some people feel more comfortable handling one sequence per file, so
   seqretsplit will be useful to them too.

   One file for each input sequence is written. The names of the files it
   creates are derived from the ID name of the sequence, followed by an
   extension denoting the format of the sequence. You have no control over
   the names of the files it writes out. For example, if the files
   embl:hsfa11* are read in and the output is specified as wibble.seq,
   then the following files are expected to be created:
hsfa110.fasta
hsfa111.fasta
hsfa112.fasta
hsfa113.fasta
hsfa114.fasta

   (No file wibble.seq is created.)

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   It shouldn't really prompt for the output filename.

   This is a side effect of the way sequence output works in EMBOSS.
   Writing multiple sequences to separate files (the -ossingle qualifier)
   does this, and seqretsplit has set it automatically on.

See also

   Program name     Description
   aligncopy        Read and write alignments
   aligncopypair    Read and write pairs from alignments
   biosed           Replace or delete sequence sections
   codcopy          Copy and reformat a codon usage table
   cutseq           Remove a section from a sequence
   degapseq         Remove non-alphabetic (e.g. gap) characters from sequences
   descseq          Alter the name or description of a sequence
   entret           Retrieve 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         Read and write a feature table
   featmerge        Merge two overlapping feature tables
   featreport       Read and write 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     Mask all ambiguity characters in nucleotide sequences with
                    N
   maskambigprot    Mask 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        Read and write (return) one set of sequences from many
   pasteseq         Insert one sequence into another
   revseq           Reverse and complement a nucleotide sequence
   seqcount         Read and count sequences
   seqret           Read and write (return) sequences
   seqretsetall     Read and write (return) many sets of sequences
   sizeseq          Sort sequences by size
   skipredundant    Remove redundant sequences from an input set
   skipseq          Read and write (return) sequences, skipping first few
   splitsource      Split sequence(s) into original source sequences
   splitter         Split sequence(s) into smaller 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      Remove vectors from the ends of nucleotide sequence(s)
   yank             Add a sequence reference (a full USA) to a list file

Author(s)

   Peter Rice
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

   Written (Jan 2000) - Peter Rice

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   The specification of the output file is not used when the output file
   names are generated automatically..

   At some point this ought to change and you will not be prompted for the
   output file at all.
