Ewan Birney

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://www.bioperl.org/MailList.shtml - 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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHORS

Aaron Mackey <amackey@virginia.edu> Lincoln Stein <lstein@cshl.org> Jason Stajich <jason@chg.mc.duke.edu>

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

next_primary_seq

 Title   : next_primary_seq
 Usage   : $seq = $stream->next_primary_seq()
 Function: returns the next sequence in the stream as a Bio::PrimarySeq
 Returns : Bio::Seq object
 Args    :

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    : Bio::Seq object