Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::SeqIO::gcg.3pm

NAME

Bio::SeqIO::gcg - GCG sequence input/output stream

SYNOPSIS

Do not use this module directly. Use it via the Bio::SeqIO class.

DESCRIPTION

This object can transform Bio::Seq objects to and from GCG flat file databases.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

   http://bugzilla.open-bio.org/
 
 

AUTHORS - Ewan Birney & Lincoln Stein

Email: <birney@ebi.ac.uk>
       <lstein@cshl.org>

CONTRIBUTORS

Jason Stajich, jason@bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

next_seq

  Title   : next_seq
  Usage   : $seq = $stream->next_seq()
  Function: returns the next sequence in the stream
  Returns : Bio::Seq object
  Args    :
 
 

write_seq

  Title   : write_seq
  Usage   : $stream->write_seq(@seq)
  Function: writes the formatted $seq object into the stream
  Returns : 1 for success and 0 for error
  Args    : array of Bio::PrimarySeqI object
 
 

GCG_checksum

  Title     : GCG_checksum
  Usage     : $cksum = $gcgio->GCG_checksum($seq);
  Function  : returns a gcg checksum for the sequence specified
 
              This method can also be called as a class method.
  Example   :
  Returns   : a GCG checksum string
  Argument  : a Bio::PrimarySeqI implementing object
 
 

_validate_checksum

  Title   : _validate_checksum
  Usage   : n/a - internal method
  Function: if parsed gcg sequence contains a checksum field
          : we compare it to a value computed here on the parsed
          : sequence. A checksum mismatch would indicate some
          : type of parsing failure occured.
          :
  Returns : 1 for success, 0 for failure
  Args    : string containing parsed seq, value of parsed cheksum