Bio::SeqIO::pir(3pm) User Contributed Perl Documentation Bio::SeqIO::pir(3pm)
NAME
Bio::SeqIO::pir - PIR 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 pir flat file databases.
Note: This does not completely preserve the PIR format - quality information about sequence is currently discarded since bioperl does not
have a mechanism for handling these encodings in sequence data.
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
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
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.
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:
https://redmine.open-bio.org/projects/bioperl/
AUTHORS
Aaron Mackey <amackey@virginia.edu> Lincoln Stein <lstein@cshl.org> Jason Stajich <jason@bioperl.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 : NONE
write_seq
Title : write_seq
Usage : $stream->write_seq(@seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Array of Bio::PrimarySeqI objects
perl v5.14.2 2012-03-02 Bio::SeqIO::pir(3pm)