
                              EMBOSS: descseq
     _________________________________________________________________
   
                                Program descseq
                                       
Function

   Alter the name or description of a sequence
   
Description

   Most sequence formats allow, at the very minimum, a name for the
   sequence and some comments to be stored in the sequence file.
   
   Rather than using an editor to alter the name or the comments, descseq
   allows you to simply change them and write out a new file with the
   changes in and the sequence left unaltered.
   
   The default action is to replace the existing name or description with
   your new one, but by using the qualifier '-append' what you enter is
   appended to the existing name or description.
   
   Note that is you append to a description, no space is inserted by
   default bewteen the existing description and your appended text - you
   have to put in a space yourself if you require one.
   
Usage

   Set the name of a sequence to "myclone23"
% descseq -seq clone23 -out clone23.seq -name "myclone23"

   Set the description of a sequence to "This is my clone number 244"
% descseq -seq xy24 -out xy24.seq -desc "This is my clone number 244"

   Append some text to the description of a sequence
% descseq -seq est.seq -out est4.seq -desc " (submitted)" -append

Command line arguments

   Mandatory qualifiers:
  [-sequence]          sequence   Sequence USA
  [-outseq]            seqout     Output sequence USA

   Optional qualifiers:
   -name               string     Name of the sequence
   -description        string     Description of the sequence

   Advanced qualifiers:
   -append             bool       This allows you to append the name or
                                  description you have given on to the end of
                                  the existing name or description of the
                                  sequence.

   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
   [-outseq]
   (Parameter 2) Output sequence USA Writeable sequence <sequence>.format
   Optional qualifiers Allowed values Default
   -name Name of the sequence Any string is accepted An empty string is
   accepted
   -description Description of the sequence Any string is accepted An
   empty string is accepted
   Advanced qualifiers Allowed values Default
   -append This allows you to append the name or description you have
   given on to the end of the existing name or description of the
   sequence. Yes/No No
   
Input file format

   Normal sequence.
   
Output file format

   The sequence file with a changed name or description.
   
Data files

   None.
   
Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with status 0.
   
Known bugs

   None noted.
   
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
   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

   Finished.
   
Target users

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