Merge github.com:bioperl/bioperl-live into amplicons

bioperl · Mar 6, 2012 · 37596a6 · 37596a6
2 parents 92eec7d + d41b38b
commit 37596a6
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Showing 2 changed files with 8 additions and 6 deletions.
diff --git a/Bio/Tools/IUPAC.pm b/Bio/Tools/IUPAC.pm
@@ -515,7 +515,10 @@ sub count {
  Function: Converts the ambiguous sequence into a regular expression that
            matches all of the corresponding ambiguous and non-ambiguous sequences.
            You can further manipulate the resulting regular expression with the
-           Bio::Tools::SeqPattern module.
+           Bio::Tools::SeqPattern module. After you are done building your
+           regular expression, you might want to compile it and make it case-
+           insensitive:
+              $re = qr/$re/i;
  Args    : none
  Return  : regular expression
 
@@ -541,7 +544,6 @@ sub regexp {
             $re .= $$iupacs[0];
         }
     }
-    $re = qr/$re/i;
     return $re;
 }
 

diff --git a/t/Tools/IUPAC.t b/t/Tools/IUPAC.t
@@ -33,23 +33,23 @@ ok $iupac = Bio::Tools::IUPAC->new( -seq => $ambiseq );
 
 ok my $regexp = $iupac->regexp;
 
-like $regexp, qr/A\[AGR\]TCGTTG\[ACGTBDHKMNRSVWY\]/, 'Regexp';
+is $regexp, 'A[AGR]TCGTTG[ACGTBDHKMNRSVWY]', 'Regexp';
 
 is $iupac->count(), 8, 'Count';
 
 my @seqs;
 while (my $uniqueseq = $iupac->next_seq()) {
     push @seqs, $uniqueseq->seq;
     is $uniqueseq->isa('Bio::PrimarySeqI'), 1;
-    like $uniqueseq->seq, $regexp;
+    like $uniqueseq->seq, qr/$regexp/i;
 }
 
 @seqs = sort @seqs;
 is_deeply \@seqs, [ 'AATCGTTGA', 'AATCGTTGC', 'AATCGTTGG', 'AATCGTTGT',
                     'AGTCGTTGA', 'AGTCGTTGC', 'AGTCGTTGG', 'AGTCGTTGT' ];
 
-like $ambiseq->seq, $regexp, 'Regexp matches ambiguous sequences';
-like 'ARTCGTTGW', $regexp;
+like $ambiseq->seq, qr/$regexp/i, 'Regexp matches ambiguous sequences';
+like 'ARTCGTTGW', qr/$regexp/i;
 
 
 # IUPAC code methods