AmpliconSearch now finds multiple amplicons

bioperl · Mar 4, 2012 · 6ff387d · 6ff387d
1 parent 882db99
commit 6ff387d
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Showing 2 changed files with 72 additions and 82 deletions.
diff --git a/Bio/Tools/AmpliconSearch.pm b/Bio/Tools/AmpliconSearch.pm
@@ -16,6 +16,8 @@ use Bio::SeqFeature::Amplicon;
 
 use base qw(Bio::Root::Root);
 
+my $template_str;
+
 
 =head1 NAME
 
@@ -148,6 +150,7 @@ sub _set_template {
       $template->primary_seq($primary_seq);
    }
    $self->{template} = $template;
+   $template_str = $self->template->seq;
    return $self->template;
 }
 
@@ -280,7 +283,6 @@ sub next_amplicon {
 
    my $amplicon;
 
-   my $seqstr = $self->template->seq;
    my $fwd_regexp = $self->forward_regexp;
    my $rev_regexp = $self->reverse_regexp;
 
@@ -289,31 +291,19 @@ sub next_amplicon {
 
    if ( defined($fwd_regexp) && not(defined $rev_regexp) ) {
       # From forward primer to end of template
-      if ($seqstr  =~ m/($fwd_regexp)/g) {
-         my $start = pos($seqstr) - length($1) + 1;
-         my $end   = length($seqstr);
+      if ($template_str  =~ m/($fwd_regexp)/g) {
+         my $start = pos($template_str) - length($1) + 1;
+         my $end   = length($template_str);
          $amplicon = $self->_create_amplicon($start, $end, $strand);
       }
 
    } elsif ( defined($fwd_regexp) && defined($rev_regexp) ) {
       # From forward to reverse primer
-#  while ( $seqstr =~ m/($fwd_regexp.*?$rev_regexp)/g ) {
-#      if ($seqstr  =~ m/($fwd_regexp.*?$rev_regexp)/g) {
-      if ($seqstr  =~ m/\G.*?($fwd_regexp.*?$rev_regexp)/g) {
-
-         #####
-         print "match: '$1'\n";
-         #####
-
-         my $end   = pos($seqstr);
+      if ($template_str  =~ m/($fwd_regexp.*?$rev_regexp)/g) {
+         my $end   = pos($template_str);
          my $start = $end - length($1) + 1;
-
-         ####
-         pos($seqstr) = $start + 2;
-         ####
-
          # Now trim the left end to obtain the shortest amplicon
-         my $ampliconstr = substr $seqstr, $start - 1, $end - $start + 1;
+         my $ampliconstr = substr $template_str, $start - 1, $end - $start + 1;
          if ($ampliconstr =~ m/$fwd_regexp.*($fwd_regexp)/g) {
             $start += pos($ampliconstr) - length($1);
          }

diff --git a/t/Tools/AmpliconSearch.t b/t/Tools/AmpliconSearch.t
@@ -2,7 +2,7 @@ BEGIN {
     use lib '.';
     use Bio::Root::Test;
 
-    test_begin(-tests => 29);
+    test_begin(-tests => 44);
 
     use_ok 'Bio::Tools::AmpliconSearch';
     use_ok 'Bio::PrimarySeq';
@@ -13,68 +13,68 @@ BEGIN {
 my ($search, $amplicon, $seq, $forward, $reverse);
 
 
-## Basic object
-
-#ok $search = Bio::Tools::AmpliconSearch->new(), 'Basic';
-#isa_ok $search, 'Bio::Tools::AmpliconSearch';
-
-
-## Forward primer only
-
-#$seq = Bio::PrimarySeq->new(
-#   -seq => 'AAACTTAAAGGAATTGACGGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACACACCGCCCGT',
-#);
-#$forward = Bio::PrimarySeq->new(
-#   -seq => 'AAACTTAAAGGAATTGACGG',
-#);
-#ok $search = Bio::Tools::AmpliconSearch->new(
-#   -template       => $seq,
-#   -forward_primer => $forward,
-#), 'Forward primer only';
-#is $search->forward_primer->seq, 'AAACTTAAAGGAATTGACGG';
-#is $search->reverse_primer, undef;
-#is $search->template->seq, 'AAACTTAAAGGAATTGACGGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACACACCGCCCGT';
-#ok $amplicon = $search->next_amplicon;
-#isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
-#is $amplicon->start, 1;
-#is $amplicon->end, 67;
-#is $amplicon->strand, 1;
-#is $amplicon->seq->seq, 'AAACTTAAAGGAATTGACGGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACACACCGCCCGT';
-#is $amplicon = $search->next_amplicon, undef;
-
-
-## Forward and reverse primers, no amplicon
-
-#$reverse = Bio::PrimarySeq->new(
-#   -seq => 'GTACACACCGCCCGT',
-#);
-#ok $search = Bio::Tools::AmpliconSearch->new(
-#   -template       => $seq,
-#   -forward_primer => $forward,
-#   -reverse_primer => $reverse,
-#), 'Two primers, no match';
-#is $search->forward_primer->seq, 'AAACTTAAAGGAATTGACGG';
-#is $search->reverse_primer->seq, 'GTACACACCGCCCGT';
-#is $search->template->seq, 'AAACTTAAAGGAATTGACGGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACACACCGCCCGT';
-#is $amplicon = $search->next_amplicon, undef;
-
-
-## Degenerate forward and reverse primers from file, single amplicon
-
-#ok $search = Bio::Tools::AmpliconSearch->new(
-#   -template    => $seq,
-#   -primer_file => test_input_file('forward_reverse_primers.fa'),
-#), 'Two degenerate primers from a file';
-#is $search->forward_primer->seq, 'AAACTYAAAKGAATTGRCGG';
-#is $search->reverse_primer->seq, 'ACGGGCGGTGTGTRC';
-#is $search->template->seq, 'AAACTTAAAGGAATTGACGGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACACACCGCCCGT';
-#ok $amplicon = $search->next_amplicon;
-#isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
-#is $amplicon->start, 1;
-#is $amplicon->end, 67;
-#is $amplicon->strand, 1;
-#is $amplicon->seq->seq, 'AAACTTAAAGGAATTGACGGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACACACCGCCCGT';
-#is $amplicon = $search->next_amplicon, undef;
+# Basic object
+
+ok $search = Bio::Tools::AmpliconSearch->new(), 'Basic';
+isa_ok $search, 'Bio::Tools::AmpliconSearch';
+
+
+# Forward primer only
+
+$seq = Bio::PrimarySeq->new(
+   -seq => 'AAACTTAAAGGAATTGACGGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACACACCGCCCGT',
+);
+$forward = Bio::PrimarySeq->new(
+   -seq => 'AAACTTAAAGGAATTGACGG',
+);
+ok $search = Bio::Tools::AmpliconSearch->new(
+   -template       => $seq,
+   -forward_primer => $forward,
+), 'Forward primer only';
+is $search->forward_primer->seq, 'AAACTTAAAGGAATTGACGG';
+is $search->reverse_primer, undef;
+is $search->template->seq, 'AAACTTAAAGGAATTGACGGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACACACCGCCCGT';
+ok $amplicon = $search->next_amplicon;
+isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
+is $amplicon->start, 1;
+is $amplicon->end, 67;
+is $amplicon->strand, 1;
+is $amplicon->seq->seq, 'AAACTTAAAGGAATTGACGGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACACACCGCCCGT';
+is $amplicon = $search->next_amplicon, undef;
+
+
+# Forward and reverse primers, no amplicon
+
+$reverse = Bio::PrimarySeq->new(
+   -seq => 'GTACACACCGCCCGT',
+);
+ok $search = Bio::Tools::AmpliconSearch->new(
+   -template       => $seq,
+   -forward_primer => $forward,
+   -reverse_primer => $reverse,
+), 'Two primers, no match';
+is $search->forward_primer->seq, 'AAACTTAAAGGAATTGACGG';
+is $search->reverse_primer->seq, 'GTACACACCGCCCGT';
+is $search->template->seq, 'AAACTTAAAGGAATTGACGGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACACACCGCCCGT';
+is $amplicon = $search->next_amplicon, undef;
+
+
+# Degenerate forward and reverse primers from file, single amplicon
+
+ok $search = Bio::Tools::AmpliconSearch->new(
+   -template    => $seq,
+   -primer_file => test_input_file('forward_reverse_primers.fa'),
+), 'Two degenerate primers from a file';
+is $search->forward_primer->seq, 'AAACTYAAAKGAATTGRCGG';
+is $search->reverse_primer->seq, 'ACGGGCGGTGTGTRC';
+is $search->template->seq, 'AAACTTAAAGGAATTGACGGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACACACCGCCCGT';
+ok $amplicon = $search->next_amplicon;
+isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
+is $amplicon->start, 1;
+is $amplicon->end, 67;
+is $amplicon->strand, 1;
+is $amplicon->seq->seq, 'AAACTTAAAGGAATTGACGGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACACACCGCCCGT';
+is $amplicon = $search->next_amplicon, undef;
 
 
 # Multiple amplicons