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:hsfa* 
Reads and writes (returns) sequences in individual files
Output sequence [hsfau.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

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-outseq]            seqoutall  Output sequence(s) USA

   Optional qualifiers: (none)
   Advanced qualifiers:
   -firstonly          boolean    Read one sequence and stop

   General qualifiers:
  -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


Mandatory qualifiers Allowed values Default
[-sequence]
(Parameter 1)
Sequence database USA Readable sequence(s) Required
[-outseq]
(Parameter 2)
Output sequence(s) USA Writeable sequence(s) <sequence>.format
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
-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:hsfa*' is a sequence entry in the example nucleic acid database 'tembl'

Output file format

Output files for usage example

File: hsfau.fasta

>HSFAU X65923.1 H.sapiens fau mRNA
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttcagtcaaaaaaaaaa

File: hsfau1.fasta

>HSFAU1 X65921.1 H.sapiens fau 1 gene
ctaccattttccctctcgattctatatgtacactcgggacaagttctcctgatcgaaaac
ggcaaaactaaggccccaagtaggaatgccttagttttcggggttaacaatgattaacac
tgagcctcacacccacgcgatgccctcagctcctcgctcagcgctctcaccaacagccgt
agcccgcagccccgctggacaccggttctccatccccgcagcgtagcccggaacatggta
gctgccatctttacctgctacgccagccttctgtgcgcgcaactgtctggtcccgccccg
tcctgcgcgagctgctgcccaggcaggttcgccggtgcgagcgtaaaggggcggagctag
gactgccttgggcggtacaaatagcagggaaccgcgcggtcgctcagcagtgacgtgaca
cgcagcccacggtctgtactgacgcgccctcgcttcttcctctttctcgactccatcttc
gcggtagctgggaccgccgttcaggtaagaatggggccttggctggatccgaagggcttg
tagcaggttggctgcggggtcagaaggcgcggggggaaccgaagaacggggcctgctccg
tggccctgctccagtccctatccgaactccttgggaggcactggccttccgcacgtgagc
cgccgcgaccaccatcccgtcgcgatcgtttctggaccgctttccactcccaaatctcct
ttatcccagagcatttcttggcttctcttacaagccgtcttttctttactcagtcgccaa
tatgcagctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaac
ggtcgcccagatcaaggtaaggctgcttggtgcgccctgggttccattttcttgtgctct
tcactctcgcggcccgagggaacgcttacgagccttatctttccctgtaggctcatgtag
cctcactggagggcattgccccggaagatcaagtcgtgctcctggcaggcgcgcccctgg
aggatgaggccactctgggccagtgcggggtggaggccctgactaccctggaagtagcag
gccgcatgcttggaggtgagtgagagaggaatgttctttgaagtaccggtaagcgtctag
tgagtgtggggtgcatagtcctgacagctgagtgtcacacctatggtaatagagtacttc
tcactgtcttcagttcagagtgattcttcctgtttacatccctcatgttgaacacagacg
tccatgggagactgagccagagtgtagttgtatttcagtcacatcacgagatcctagtct
ggttatcagcttccacactaaaaattaggtcagaccaggccccaaagtgctctataaatt
agaagctggaagatcctgaaatgaaacttaagatttcaaggtcaaatatctgcaactttg
ttctcattacctattgggcgcagcttctctttaaaggcttgaattgagaaaagaggggtt
ctgctgggtggcaccttcttgctcttacctgctggtgccttcctttcccactacaggtaa
agtccatggttccctggcccgtgctggaaaagtgagaggtcagactcctaaggtgagtga
gagtattagtggtcatggtgttaggactttttttcctttcacagctaaaccaagtccctg
ggctcttactcggtttgccttctccctccctggagatgagcctgagggaagggatgctag
gtgtggaagacaggaaccagggcctgattaaccttcccttctccaggtggccaaacagga
gaagaagaagaagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgt
caacgttgtgcccacctttggcaagaagaagggccccaatgccaactcttaagtcttttg
taattctggctttctctaataaaaaagccacttagttcagtcatcgcattgtttcatctt
tacttgcaaggcctcagggagaggtgtgcttctcgg

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.

See also

Program nameDescription
biosedReplace or delete sequence sections
cutseqRemoves a specified section from a sequence
degapseqRemoves gap characters from sequences
descseqAlter the name or description of a sequence
entretReads and writes (returns) flatfile entries
extractfeatExtract features from a sequence
extractseqExtract regions from a sequence
listorWrites a list file of the logical OR of two sets of sequences
maskfeatMask off features of a sequence
maskseqMask off regions of a sequence
newseqType in a short new sequence
noreturnRemoves carriage return from ASCII files
notseqExcludes a set of sequences and writes out the remaining ones
nthseqWrites one sequence from a multiple set of sequences
pasteseqInsert one sequence into another
revseqReverse and complement a sequence
seqretReads and writes (returns) sequences
skipseqReads and writes (returns) sequences, skipping the first few
splitterSplit a sequence into (overlapping) smaller sequences
trimestTrim poly-A tails off EST sequences
trimseqTrim ambiguous bits off the ends of sequences
unionReads sequence fragments and builds one sequence
vectorstripStrips out DNA between a pair of vector sequences
yankReads a sequence range, appends the full USA to a list file

Author(s)

This application was written by Peter Rice (price@hgmp.mrc.ac.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