Provided by: libbio-perl-perl_1.7.2-3_all
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: <email@example.com> <firstname.lastname@example.org>
Jason Stajich, email@example.com
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 occurred. : Returns : 1 for success, 0 for failure Args : string containing parsed seq, value of parsed checksum