
                                 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.

   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. In
   this case, memory usage may be reduced by repeating the analysis
   several times on split sub-sequences.

   If you need to split a large sequence into smaller subsequences so
   that a non-EMBOSS program can analyse the smaller sequence, it may
   also be useful to write the sub-sequences into separate files instead
   of the default EMBOSS behaviour of concatenating them together into
   one file.

   To write the output sequences to separate files, use the command-line
   switch '-ossingle'.

Usage

   Here is a sample session with splitter

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


% splitter tembl:BA000025 ba000025.split 
Split a sequence into (overlapping) smaller sequences

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

   Example 2

   Split a sequence into sub-sequences of 50,000 bases with an overlap of
   3,000 bases on each sub-sequence:


% splitter tembl:BA000025 ba000025.split -size=50000 -over=3000 
Split a sequence into (overlapping) smaller sequences

   Go to the output files for this example

Command line arguments

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

   Additional (Optional) qualifiers:
   -size               integer    [10000] Size to split at (Integer 1 or more)
   -overlap            integer    [0] Overlap between split sequences (Integer
                                  0 or more)
   -source             boolean    [N] Split using source features with /origid
                                  qualifiers
   -multifile          boolean    [N] Split sequence into multiple files

   Advanced (Unprompted) qualifiers:
   -feature            boolean    [N] Use feature information
   -addoverlap         boolean    [N] Add overlap to size

   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

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

   None.

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
   seqretsplit  Reads and writes (returns) sequences in individual files
   skipseq      Reads and writes (returns) sequences, skipping first few
   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)

   Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

   Completed 22 March 1999

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

Comments

   None
