EMBOSS: seqretsplit

| seqretsplit

## Function

Reads and writes (returns) sequences in individual files

## Description

seqretsplit is exactly the same as the program seqret except that when it writes out more than one sequence, it writes each sequence to an individual file.

Its main use is therefore to split a file containing multiple sequences into many files, each containing one sequence.

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.)

Why would you want to split a multiple sequence file into many individual files?

EMBOSS programs can read in many sequences from one file where this is sensible. Sometimes EMBOSS programs can only read in one sequence at a time because that is the sensible way to do things, but your sequence is one sequence of many in a file. You can specify that sequence using the USA filename:sequenceID, but you may still feel more comfortable splitting your sequences up into many files first.

Many non-EMBOSS programs will also have restrictions on whether they can read in multiple sequence files or not.

## Usage

Here is a sample session with seqretsplit

    % seqretsplit tembl:m1190*
    Reads and writes (returns) sequences in 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

       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
       -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 standard output
       -filter             boolean    Read standard input, write 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. 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

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | (Gapped) sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
[-outseq] (Parameter 2) | Sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format
Additional (Optional) qualifiers | Allowed values | Default
(none)
Advanced (Unprompted) qualifiers | Allowed values | Default
-feature | Use feature information | Boolean value Yes/No | No
-firstonly | Read one sequence and stop | Boolean value Yes/No | No

## Input file format

seqretsplit reads a normal sequence USA.

### Input files for usage example

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

## Output file format

### Output files for usage example

### File: m11903.fasta

    >M11903 M11903.1 Rattus norvegicus androgen-responsive protein precursor (Svf) gene, 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) gene, 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) gene, 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

None.

## 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 isa side effect of the waysequence 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
--- | ---
biosed | Replace or delete sequence sections
codcopy | Reads and writes a codon usage table
cutseq | Removes a specified section from a sequence
degapseq | Removes gap characters from sequences
descseq | Alter the name or description of a sequence
entret | Reads and writes (returns) flatfile entries
extractalign | Extract regions from a sequence alignment
extractfeat | Extract features from a sequence
extractseq | Extract regions from a sequence
listor | Write a list file of the logical OR of two sets of sequences
makenucseq | Creates random nucleotide sequences
makeprotseq | Creates random protein sequences
maskfeat | Mask off features of a sequence
maskseq | Mask off regions of a sequence
newseq | Type in a short new sequence
noreturn | Removes carriage return from ASCII files
notseq | Exclude a set of sequences and write out the remaining ones
nthseq | Writes one sequence from a multiple set of sequences
pasteseq | Insert one sequence into another
revseq | Reverse and complement a sequence
seqret | Reads and writes (returns) sequences
skipseq | Reads and writes (returns) sequences, skipping first few
splitter | Split a sequence into (overlapping) smaller sequences
trimest | Trim poly-A tails off EST sequences
trimseq | Trim ambiguous bits off the ends of sequences
union | Reads sequence fragments and builds one sequence
vectorstrip | Strips out DNA between a pair of vector sequences
yank | Reads a sequence range, appends the full USA to a list file

## Author(s)

Peter Rice (pmr © ebi.ac.uk)
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

## 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.