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>
9 # You may distribute this module under the same terms as perl itself
11 # POD documentation - main docs before the code
15 Bio::Tools::Promoterwise - parser for Promoterwise tab format output
19 use Bio::Tools::Promoterwise;
21 my $pw = Bio::Tools::Promoterwise->new(-file=>"out",
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";
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";
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.
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
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.
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
76 https://github.com/bioperl/bioperl-live/issues
78 =head1 AUTHOR - Shawn Hoon
80 Email shawnh@fugu-sg.org
84 The rest of the documentation details each of the object methods.
85 Internal methods are usually preceded with a _
90 # Let the code begin...
93 package Bio
::Tools
::Promoterwise
;
96 use Bio
::SeqFeature
::FeaturePair
;
97 use Bio
::SeqFeature
::Generic
;
99 use base
qw(Bio::Root::Root Bio::Root::IO);
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 => $val, # for initing input, see Bio::Root::IO
113 my($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);
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>
137 $self->_parse unless $self->_parsed;
138 return $self->_next_result;
144 while (defined($_ = $self->_readline()) ) {
147 push @
{$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};
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);
179 my $sub1 = Bio
::SeqFeature
::Generic
->new(-start
=>$start_1,
183 -primary
=>"conserved_element",
184 -source_tag
=>"promoterwise",
186 $sub1->attach_seq($self->query1_seq) if $self->query1_seq;
188 my $sub2 = Bio
::SeqFeature
::Generic
->new(-start
=>$start_2,
192 -primary
=>"conserved_element",
193 -source_tag
=>"promoterwise",
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,
204 $self->_feature_pairs(\
@fp);
212 $self->{'_feature_pairs'} = $fp;
214 return $self->{'_feature_pairs'};
219 return unless (exists($self->{'_feature_pairs'}) && @
{$self->{'_feature_pairs'}});
220 return shift(@
{$self->{'_feature_pairs'}});
223 my ($self,$flag) = @_;
225 $self->{'_flag'} = 1;
227 return $self->{'_flag'};
231 my ($self,$val) = @_;
233 $self->{'query1_seq'} = $val;
235 return $self->{'query1_seq'};
238 my ($self,$val) = @_;
240 $self->{'query2_seq'} = $val;
242 return $self->{'query2_seq'};