Sendu Bala
and 1 contributors


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.


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AUTHORS - Ewan Birney & Lincoln Stein

Email: <> <>


Jason Stajich,


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 occured.
 Returns : 1 for success, 0 for failure
 Args    : string containing parsed seq, value of parsed cheksum