Bio::Tools::PromoterwiUser)Contributed Perl DocumenBio::Tools::Promoterwise(3)NAMEBio::Tools::Promoterwise - parser for Promoterwise tab format output
SYNOPSIS
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
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 - Shawn Hoon
Email shawnh@fugu-sg.org
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::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
perl v5.14.1 2011-07-22 Bio::Tools::Promoterwise(3)