Bio::SeqIO::pir(3)

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

  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
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