Bio::Tools::Phylo::Gumby - Parses output from gumby
#!/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();
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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