
                               EMBOSS: cutseq
     _________________________________________________________________
   
                                Program cutseq
                                       
Function

   Removes a specified section from a sequence
   
Description

   This simple editing program allows you to cut out a region from your
   sequence by specifying the begin and end positions of the sequence to
   remove.
   
   It removes the sequence from the specified start to the end positions
   (inclusive) and returns the rest of the sequence in the output file.
   
Usage

   To remove bases 10 to 12 from a sequence 'gatta.seq' and write to the
   new sequence file 'gatta2.seq':
% cutseq gatta.seq gatta2.seq -from=10 -to=12

   To remove the first 20 bases from 'hatta.seq' and write it to
   'jsh.seq':
% cutseq -seq=hatta.seq -from=1 -to=20 -out=jsh.seq

Command line arguments

   Mandatory qualifiers:
  [-sequence]          sequence   Sequence USA
   -from               integer    This is the start position (inclusive) of
                                  the section of the sequence that you wish to
                                  remove.
   -to                 integer    This is the end position (inclusive) of the
                                  section of the sequence that you wish to
                                  remove.
  [-outseq]            seqout     Output sequence USA

   Optional qualifiers: (none)
   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 USA Readable sequence Required
   -from This is the start position (inclusive) of the section of the
   sequence that you wish to remove. Any integer value Start of sequence
   (0)
   -to This is the end position (inclusive) of the section of the
   sequence that you wish to remove. Any integer value End of sequence
   (0)
   [-outseq]
   (Parameter 2) Output sequence USA Writeable sequence <sequence>.format
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

   Single sequence.
   
Output file format

   Single sequence file.
   
Data files

   None.
   
Notes

   This can be used as a simple sequence editor.
   
References

   None.
   
Warnings

   You can delete a complete sequence and write out an empty sequence
   file.
   
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
   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
   splitter     Split a sequence into (overlapping) smaller sequences
   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 26 Jan 1999
   
Target users

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