Rechercher une page de manuel
Bio::SeqIO::gcg.3pm
Langue: en
Version: 2008-01-11 (mandriva - 01/05/08)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::SeqIO::gcg - GCG sequence input/output streamSYNOPSIS
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://bioperl.org/wiki/Mailing_lists - About the mailing lists
Reporting 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 the web:
http://bugzilla.open-bio.org/
AUTHORS - Ewan Birney & Lincoln Stein
Email: <birney@ebi.ac.uk><lstein@cshl.org>
CONTRIBUTORS
Jason Stajich, jason@bioperl.orgAPPENDIX
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 occured. : Returns : 1 for success, 0 for failure Args : string containing parsed seq, value of parsed cheksum
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre