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Bio::SeqIO::gcg(3) User Contributed Perl Documentation Bio::SeqIO::gcg(3)

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

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

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

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

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.

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:

  https://github.com/bioperl/bioperl-live/issues

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

Jason Stajich, jason@bioperl.org

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

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

 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

 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

 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 occurred.
         :
 Returns : 1 for success, 0 for failure
 Args    : string containing parsed seq, value of parsed checksum
2019-12-07 perl v5.32.1

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