NAME¶
Bio::AlignIO::psi - Read/Write PSI-BLAST profile alignment files
SYNOPSIS¶
This module will parse PSI-BLAST output of the format seqid XXXX
DESCRIPTION¶
This is a parser for psi-blast blocks.
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 the Bioperl mailing
list. 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 of the bugs
and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Jason Stajich¶
Email jason@bioperl.org
APPENDIX¶
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
new¶
Title : new
Usage : my $obj = Bio::AlignIO::psi->new();
Function: Builds a new Bio::AlignIO::psi object
Returns : Bio::AlignIO::psi
Args :
next_aln¶
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream
Returns : Bio::Align::AlignI object
Args : NONE
See Bio::Align::AlignI
write_aln¶
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the NCBI psi-format object (.aln) into the stream
Returns : 1 for success and 0 for error
Args : Bio::Align::AlignI object
Bio::Align::AlignI