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Bio::AlignIO::emboss.3pm
Langue: en
Version: 2010-05-19 (ubuntu - 24/10/10)
Section: 3 (Bibliothèques de fonctions)
Sommaire
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:http://bugzilla.open-bio.org/
AUTHOR - Jason Stajich
Email jason@bioperl.orgAPPENDIX
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
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre