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Bio::Tools::Promoterwise.3pm
Langue: en
Version: 2009-03-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Promoterwise - parser for Promoterwise tab format outputSYNOPSIS
use Bio::Tools::Promoterwise; my $pw = Bio::Tools::Promoterwise->new(-file=>"out", -query1_seq=>$seq1, -query2_seq=>$seq2); while (my $fp = $pw->next_result){ print "Hit Length: ".$fp->feature1->length."\n"; print "Hit Start: ".$fp->feature1->start."\n"; print "Hit End: ".$fp->feature1->end."\n"; print "Hsps: \n"; my @first_hsp = $fp->feature1->sub_SeqFeature; my @second_hsp = $fp->feature2->sub_SeqFeature; foreach my $i (0..$#first_hsp){ print $first_hsp[$i]->start. " ".$first_hsp[$i]->end." ". $second_hsp[$i]->start. " ".$second_hsp[$i]->end."\n"; } }
DESCRIPTION
Promoteriwise is an alignment algorithm that relaxes the constraint that local alignments have to be co-linear. Otherwise it provides a similar model to DBA, which is designed for promoter sequence alignments. Promoterwise is written by Ewan Birney. It is part of the wise2 package available at <ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/>This module is the parser for the Promoterwise output in tab format.
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
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 - Shawn Hoon
Email shawnh@fugu-sg.orgAPPENDIX
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::Promoterwise->new(); Function: Builds a new Bio::Tools::Promoterwise object Returns : L<Bio::Tools::Promoterwise> Args : -fh/-file => $val, # for initing input, see Bio::Root::IO
next_result
Title : next_result Usage : my $r = $rpt_masker->next_result Function: Get the next result set from parser data Returns : an L<Bio::SeqFeature::FeaturePair> Args : none
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