Bio::AlignIO::emboss(3pm) User Contributed Perl Documentation Bio::AlignIO::emboss(3pm)
NAME
Bio::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle)
SYNOPSIS
# do not use the object directly
use Bio::AlignIO;
# read in an alignment from the EMBOSS program water
my $in = Bio::AlignIO->new(-format => 'emboss',
-file => 'seq.water');
while( my $aln = $in->next_aln ) {
# do something with the alignment
}
DESCRIPTION
This object handles parsing and writing pairwise sequence alignments from the EMBOSS suite.
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://redmine.open-bio.org/projects/bioperl/
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 _
next_aln
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream.
Returns : L<Bio::Align::AlignI> object - returns 0 on end of file
or on error
Args : NONE
write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in emboss format
Returns : 1 for success and 0 for error
Args : L<Bio::Align::AlignI> object
perl v5.14.2 2012-03-02 Bio::AlignIO::emboss(3pm)