|Bio::SeqIO::gcg(3pm)||User Contributed Perl Documentation||Bio::SeqIO::gcg(3pm)|
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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Please direct usage questions or support issues to the mailing list:
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.
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AUTHORS - Ewan Birney & Lincoln Stein¶
Jason Stajich, email@example.com
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