maint: restructure to use Dist::Zilla
[bioperl-live.git] / lib / Bio / Tools / Promoterwise.pm
blobd112189e568f664e13407cef41a3cb1251df8a82
1 # BioPerl module for Bio::Tools::Promoterwise
3 # Please direct questions and support issues to <bioperl-l@bioperl.org>
5 # Cared for by Shawn Hoon <shawnh@fugu-sg.org>
7 # Copyright Shawn Hoon
9 # You may distribute this module under the same terms as perl itself
11 # POD documentation - main docs before the code
13 =head1 NAME
15 Bio::Tools::Promoterwise - parser for Promoterwise tab format output
17 =head1 SYNOPSIS
19 use Bio::Tools::Promoterwise;
21 my $pw = Bio::Tools::Promoterwise->new(-file=>"out",
22 -query1_seq=>$seq1,
23 -query2_seq=>$seq2);
24 while (my $fp = $pw->next_result){
25 print "Hit Length: ".$fp->feature1->length."\n";
26 print "Hit Start: ".$fp->feature1->start."\n";
27 print "Hit End: ".$fp->feature1->end."\n";
28 print "Hsps: \n";
29 my @first_hsp = $fp->feature1->sub_SeqFeature;
30 my @second_hsp = $fp->feature2->sub_SeqFeature;
31 foreach my $i (0..$#first_hsp){
32 print $first_hsp[$i]->start. " ".$first_hsp[$i]->end." ".
33 $second_hsp[$i]->start. " ".$second_hsp[$i]->end."\n";
37 =head1 DESCRIPTION
39 Promoteriwise is an alignment algorithm that relaxes the constraint
40 that local alignments have to be co-linear. Otherwise it provides a
41 similar model to DBA, which is designed for promoter sequence
42 alignments. Promoterwise is written by Ewan Birney. It is part of
43 the wise2 package available at
44 L<ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/>
46 This module is the parser for the Promoterwise output in tab format.
48 =head1 FEEDBACK
50 =head2 Mailing Lists
52 User feedback is an integral part of the evolution of this and other
53 Bioperl modules. Send your comments and suggestions preferably to
54 the Bioperl mailing list. Your participation is much appreciated.
56 bioperl-l@bioperl.org - General discussion
57 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
59 =head2 Support
61 Please direct usage questions or support issues to the mailing list:
63 I<bioperl-l@bioperl.org>
65 rather than to the module maintainer directly. Many experienced and
66 reponsive experts will be able look at the problem and quickly
67 address it. Please include a thorough description of the problem
68 with code and data examples if at all possible.
70 =head2 Reporting Bugs
72 Report bugs to the Bioperl bug tracking system to help us keep track
73 of the bugs and their resolution. Bug reports can be submitted via the
74 web:
76 https://github.com/bioperl/bioperl-live/issues
78 =head1 AUTHOR - Shawn Hoon
80 Email shawnh@fugu-sg.org
82 =head1 APPENDIX
84 The rest of the documentation details each of the object methods.
85 Internal methods are usually preceded with a _
87 =cut
90 # Let the code begin...
93 package Bio::Tools::Promoterwise;
94 use strict;
96 use Bio::SeqFeature::FeaturePair;
97 use Bio::SeqFeature::Generic;
99 use base qw(Bio::Root::Root Bio::Root::IO);
101 =head2 new
103 Title : new
104 Usage : my $obj = Bio::Tools::Promoterwise->new();
105 Function: Builds a new Bio::Tools::Promoterwise object
106 Returns : L<Bio::Tools::Promoterwise>
107 Args : -fh/-file => $val, # for initing input, see Bio::Root::IO
110 =cut
112 sub new {
113 my($class,@args) = @_;
115 my $self = $class->SUPER::new(@args);
116 $self->_initialize_io(@args);
117 my ($query1,$query2) = $self->_rearrange([qw(QUERY1_SEQ QUERY2_SEQ)],@args);
118 $self->query1_seq($query1) if ($query1);
119 $self->query2_seq($query2) if ($query2);
121 return $self;
124 =head2 next_result
126 Title : next_result
127 Usage : my $r = $rpt_masker->next_result
128 Function: Get the next result set from parser data
129 Returns : an L<Bio::SeqFeature::FeaturePair>
130 Args : none
133 =cut
135 sub next_result {
136 my ($self) = @_;
137 $self->_parse unless $self->_parsed;
138 return $self->_next_result;
141 sub _parse{
142 my ($self) = @_;
143 my (%hash,@fp);
144 while (defined($_ = $self->_readline()) ) {
145 chomp;
146 my @array = split;
147 push @{$hash{$array[-1]}}, \@array;
149 foreach my $key(keys %hash){
150 my $sf1 = Bio::SeqFeature::Generic->new(-primary=>"conserved_element",
151 -source_tag=>"promoterwise");
152 $sf1->attach_seq($self->query1_seq) if $self->query1_seq;
153 my $sf2 = Bio::SeqFeature::Generic->new(-primary=>"conserved_element",
154 -source_tag=>"promoterwise");
155 $sf2->attach_seq($self->query2_seq) if $self->query2_seq;
156 foreach my $info(@{$hash{$key}}){
158 my ($score,$id1,$start_1,$end_1, $strand_1,$s1_len,
159 $id2,$start_2,$end_2,$strand_2,$s2_len, $group);
160 if( @{$info} == 12 ) {
161 ($score,$id1,$start_1,$end_1, $strand_1,$s1_len,
162 $id2,$start_2,$end_2,$strand_2,$s2_len, $group) = @{$info};
163 } elsif( @{$info} == 10 ) {
164 ($score,$id1,$start_1,$end_1, $strand_1,
165 $id2,$start_2,$end_2,$s2_len, $group) = @{$info};
166 } else {
167 $self->throw("unknown promoterwise output, ", scalar @{$info},
168 " columns, expected 10 or 12\n");
170 if(!$sf1->strand && !$sf2->strand){
171 $sf1->strand($strand_1);
172 $sf2->strand($strand_2);
173 $sf1->seq_id($id1);
174 $sf2->seq_id($id2);
175 $sf1->score($score);
176 $sf2->score($score);
179 my $sub1 = Bio::SeqFeature::Generic->new(-start=>$start_1,
180 -seq_id=>$id1,
181 -end =>$end_1,
182 -strand=>$strand_1,
183 -primary=>"conserved_element",
184 -source_tag=>"promoterwise",
185 -score=>$score);
186 $sub1->attach_seq($self->query1_seq) if $self->query1_seq;
188 my $sub2 = Bio::SeqFeature::Generic->new(-start=>$start_2,
189 -seq_id=>$id2,
190 -end =>$end_2,
191 -strand=>$strand_2,
192 -primary=>"conserved_element",
193 -source_tag=>"promoterwise",
194 -score=>$score);
195 $sub2->attach_seq($self->query2_seq) if $self->query2_seq;
196 $sf1->add_SeqFeature($sub1,'EXPAND');
197 $sf2->add_SeqFeature($sub2,'EXPAND');
200 my $fp = Bio::SeqFeature::FeaturePair->new(-feature1=>$sf1,
201 -feature2=>$sf2);
202 push @fp, $fp;
204 $self->_feature_pairs(\@fp);
205 $self->_parsed(1);
206 return;
209 sub _feature_pairs {
210 my ($self,$fp) = @_;
211 if($fp){
212 $self->{'_feature_pairs'} = $fp;
214 return $self->{'_feature_pairs'};
217 sub _next_result {
218 my ($self) = @_;
219 return unless (exists($self->{'_feature_pairs'}) && @{$self->{'_feature_pairs'}});
220 return shift(@{$self->{'_feature_pairs'}});
222 sub _parsed {
223 my ($self,$flag) = @_;
224 if($flag){
225 $self->{'_flag'} = 1;
227 return $self->{'_flag'};
230 sub query1_seq {
231 my ($self,$val) = @_;
232 if($val){
233 $self->{'query1_seq'} = $val;
235 return $self->{'query1_seq'};
237 sub query2_seq {
238 my ($self,$val) = @_;
239 if($val){
240 $self->{'query2_seq'} = $val;
242 return $self->{'query2_seq'};