
                              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
