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://www.bioperl.org/MailList.shtml - About the mailing listsReporting 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 email or the web:
bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/AUTHORS - Ewan Birney & Lincoln Stein
Email: <birney@ebi.ac.uk> <lstein@cshl.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 fromatted $seq object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq object, sequence stringGCG_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