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bio::tools::phylo::gumby(3pm) [debian man page]

Bio::Tools::Phylo::Gumby(3pm)				User Contributed Perl Documentation			     Bio::Tools::Phylo::Gumby(3pm)

NAME
Bio::Tools::Phylo::Gumby - Parses output from gumby SYNOPSIS
#!/usr/bin/perl -Tw use strict; use Bio::Tools::Phylo::Gumby; my $parser = Bio::Tools::Phylo::Gumby->new(-file => "out.align"); my @features = $parser->next_result(); DESCRIPTION
This module is used to parse the output from 'gumby' by Shyam Prabhakar. You can get details here: http://pga.lbl.gov/gumby/ It works on the .align files produced. The result is a list of feature objects. 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 - Sendu Bala Email bix@sendu.me.uk 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::Tools::Phylo::Gumby->new(); Function: Builds a new Bio::Tools::Phylo::Gumby object Returns : Bio::Tools::Phylo::Gumby Args : -file (or -fh) should contain the contents of a gumby .align output file next_result Title : next_result Usage : $result = $obj->next_result(); Function: Returns the next set of results available from the input, or undef if there are no more results. Returns : list of Bio::SeqFeature::Annotated (one per sequence). Features are annotated with tags for pvalue and 'kind' (holding 'all', 'exon', or 'nonexon'). NB: Gumby ignores sequence coordinates in input alignments, treating each sequence as if it started at position 1. If you're running this manually (ie. not via the Bio::Tools::Run::Phylo::Gumby) you will have to adjust the coordinates to match up with your input alignment and sequences. Args : none perl v5.14.2 2012-03-02 Bio::Tools::Phylo::Gumby(3pm)

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Bio::Tools::Match(3pm)					User Contributed Perl Documentation				    Bio::Tools::Match(3pm)

NAME
Bio::Tools::Match - Parses output from Transfac's match(TM) SYNOPSIS
use strict; use Bio::Tools::Match; my $parser = Bio::Tools::Match->new(-file => "match.out"); while (my $feat = $parser->next_result) { my $start = $feat->start; my $end = $feat->end; my $core_score = $feat->score; my $matrix_score = ($feat->annotation->get_Annotations('matrix_score'))[0]->value; my $matrix_id = ($feat->annotation->get_Annotations('matrix_id'))[0]->value; } DESCRIPTION
This module is used to parse the output from Transfac's match(TM) program. It doesn't support the histogram output of match. Each result is a Bio::SeqFeature::Annotated representing a single matrix match. 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 - Sendu Bala Email bix@sendu.me.uk 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::Tools::Match->new(); Function: Builds a new Bio::Tools::Match object Returns : Bio::Tools::Match Args : -file (or -fh) should contain the contents of a standard match output next_result Title : next_result Usage : $result = $obj->next_result(); Function: Returns the next result available from the input, or undef if there are no more results. Returns : Bio::SeqFeature::Annotated object. Features are annotated with tags for 'matrix_score', 'matrix_id' and a 'predicted' tag. Args : none perl v5.14.2 2012-03-02 Bio::Tools::Match(3pm)
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