EMBOSS: splitter

| ## EMBOSS: splitter

# Program splitter

## Function

Split a sequence into (overlapping) smaller sequences

## Description

This simple editing program allows you to split a long sequence into smaller, optionally overlapping, subsequences.

## Usage

To split a sequence into sub-sequences of 10,000 bases (the default size) with no overlap between the sub-sequences:

    	% splitter one_huge.seq many_small.seq

To split a sequence into sub-sequences of 50,000 bases with an overlap of 3,000 bases on each sub-sequence.

    	% splitter one_huge.seq many_small.seq -size=50000 -over=3000

## Command line arguments

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

       Optional qualifiers:
       -size               integer    Size to split at
       -overlap            integer    Overlap between split sequences

       Advanced qualifiers: (none)
       General qualifiers:
      -help                bool       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
-size | Size to split at | Integer 1 or more | 10000
-overlap | Overlap between split sequences | Integer 0 or more | 0
Advanced qualifiers | Allowed values | Default
(none)

## Input File Format

One or more sequences

## Output File Format

Many sequences.

The names of the sequences are the same as the original sequence, with '_start-end' appended, where 'start', and 'end' are the start and end positions of the sub-sequence. eg: The name HSHBB would be changed in the sub-sequences to: HSHBB_1-50000 and HSHBB_50001-73308 if they were split at the size of 50000 with no overlap.

## Data files

None.

## Notes

There should be little requirement to split sequences into smaller sub-sequences in EMBOSS, but there may be circumstances where memory usage becomes restrictive when dealing with truly large sequences.

## References

None

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0

## Known bugs

Bugs noted but not yet fixed. None.

## See also

Program name | Description
--- | ---
biosed | Replace or delete sequence sections
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
extractfeat | Extract features from a sequence
extractseq | Extract regions from a sequence
listor | Writes a list file of the logical OR of two sets of 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 | Excludes a set of sequences and writes 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
seqretsplit | Reads and writes (returns) sequences in individual files
swissparse | Retrieves sequences from swissprot using keyword search
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)

This application was written by Gary Williams (gwilliam@hgmp.mrc.ac.uk)

## History

Completed 22 March 1999
23 May 2001 - Gary Williams - changed the overlap so that the start of a new sequence section is one more than the split-point, the end is the split-point plus the overlap. e.g. splitting at 10000 with an overlap of 100 gives: 1-10100, 10001-20100, etc.

## Target users

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

## Comments