| Bio::Tools::Promoterwise(3pm) | User Contributed Perl Documentation | Bio::Tools::Promoterwise(3pm) |
Bio::Tools::Promoterwise - parser for Promoterwise tab format output
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";
}
}
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.
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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.
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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::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
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
| 2021-08-15 | perl v5.32.1 |