diff variant_effect_predictor/Bio/Tools/FootPrinter.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tools/FootPrinter.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,254 @@
+# BioPerl module for Bio::Tools::FootPrinter
+#
+# Cared for by Shawn Hoon <[e-mail]>
+#
+# Copyright Shawn Hoon
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Tools::FootPrinter - DESCRIPTION of Object
+
+=head1 SYNOPSIS
+
+    use Bio::Tools::FootPrinter;
+
+    my $tool = Bio::Tools::FootPrinter->new(-file=>"footprinter.out");
+
+    while (my $result = $tool->next_feature){
+      foreach my $feat($result->sub_SeqFeature){
+        print $result->seq_id."\t".$feat->start."\t".$feat->end."\t".$feat->seq->seq."\n";
+      }
+    }
+
+=head1 DESCRIPTION
+
+A parser for FootPrinter  output 
+
+=head1 FEEDBACK
+
+=head2 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.
+
+  [e-mail]              - General discussion
+  http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 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
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Shawn Hoon 
+
+Email [e-mail] 
+
+Describe contact details here
+
+=head1 CONTRIBUTORS
+
+Additional contributors names and emails here
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::Tools::FootPrinter;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Root::Root;
+use Bio::SeqFeature::Generic;
+use Bio::PrimarySeq;
+use Bio::Root::IO;
+
+@ISA = qw(Bio::Root::Root Bio::Root::IO );
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Tools::FootPrinter();
+ Function: Builds a new Bio::Tools::FootPrinter object 
+ Returns : Bio::Tools::FootPrinter
+ Args    : -fh/-file => $val, # for initing input, see Bio::Root::IO
+
+=cut
+
+sub new {
+  my($class,@args) = @_;
+
+  my $self = $class->SUPER::new(@args);
+  $self->_initialize_io(@args);
+
+  return $self;
+}
+
+=head2 next_feature
+
+ Title   : next_feature
+ Usage   : my $r = $footprint->next_feature
+ Function: Get the next feature from parser data
+ Returns : L<Bio::SeqFeature::Generic> 
+ Args    : none
+
+=cut
+
+sub next_feature{
+   my ($self) = @_;
+   $self->_parse_predictions() unless $self->_predictions_parsed();
+   return shift @{$self->{'_feature'}};
+
+}
+
+=head2 _add_feature
+
+ Title   : _add_feature
+ Usage   : $footprint->_add_feature($feat)
+ Function: Add feature to array
+ Returns : none
+ Args    : none
+
+=cut
+
+sub _add_feature {
+    my ($self,$feat) = @_;
+    if($feat){
+        push @{$self->{'_feature'}},$feat;
+    }
+}
+
+=head2 _parse_predictions
+
+ Title   : _parse_predictions
+ Usage   : my $r = $footprint->_parse_predictions
+ Function: do the parsing 
+ Returns : none 
+ Args    : none
+
+=cut
+
+sub _parse_predictions {
+  my ($self) = @_;
+  $/="";
+  my ($seq,$third,$name);
+  while ($_ = $self->_readline) {
+    chomp;
+    my @array = split("\n",$_);
+    if($#array == 3){
+        if($name){
+            $name=~s/>//;
+            my $feat = $self->_parse($name,$seq,$third);
+            $self->_add_feature($feat);
+        }
+        $name = shift @array;
+        $seq=$array[0];
+        $third=$array[2];
+        next;
+    }
+    $seq.=$array[0];
+    $third.=$array[2];
+  }
+  $name=~s/>//;
+  my $feat = $self->_parse($name,$seq,$third);
+  $self->_add_feature($feat);
+
+  $self->_predictions_parsed(1);
+}
+
+=head2 _predictions_parsed
+
+ Title   : _predictions_parsed
+ Usage   : $footprint->_predictions_parsed(1)
+ Function: Get/Set for whether predictions parsed
+ Returns : 1/0
+ Args    : none
+
+=cut
+
+sub _predictions_parsed {
+    my ($self,$val) = @_;
+    if($val){
+        $self->{'_predictions_parsed'} = $val;
+    }
+    return $self->{'_predictions_parsed'};
+}
+
+
+=head2 _parse
+
+ Title   : _parse
+ Usage   : $footprint->_parse($name,$seq,$pattern)
+ Function: do the actual parsing
+ Returns : L<Bio::SeqFeature::Generic>
+ Args    : none
+
+=cut
+
+sub _parse {
+  my ($self,$name,$seq,$pattern) = @_;
+    my @char = split('',$pattern);
+    my $prev;
+   my $word;
+    my @words;
+    foreach my $c(@char){
+        if(!$word){
+            $word .= $c;
+            $prev = $c;
+            next;
+        }
+        if ($c eq $prev){
+          $word.=$c;
+          $prev = $c;
+        }
+        else {
+            #remove words with only \s
+            $word=~s/\s+//g;
+            if ($word ne ''){
+              push @words, $word;
+            }
+            $word=$c;
+           $prev = $c;
+           
+        }
+    }
+    $word=~s/\s+//g;
+    if($word ne ''){
+      push @words, $word;
+    }
+    my $last;
+    my $feat = new Bio::SeqFeature::Generic(-seq_id=>$name);
+    my $offset=0;
+    foreach my $w(@words){
+        if($w !~ /^$/){
+          my $index = index($pattern,$w,$offset);
+          $offset = $index + length($w);
+          my $subfeat = new Bio::SeqFeature::Generic ( -seq_id=>$name,
+                                                    -start => $index+1, 
+                                                    -end =>$index+length($w),
+                                                    -source=>"FootPrinter");
+          $feat->add_sub_SeqFeature($subfeat,'EXPAND');
+        }
+    }
+    my $priseq = Bio::PrimarySeq->new(-id=>$name,-seq=>$seq);
+    $feat->attach_seq($priseq);
+    return $feat;
+    
+}
+
+1;