NAME¶
Bio::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:
https://github.com/bioperl/bioperl-live/issues
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