Merge branch 'master' of github.com:bioperl/bioperl-live

bioperl · Mar 5, 2011 · 7407a26 · 7407a26
2 parents b774330 + 6a79bde
commit 7407a26
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Showing 3 changed files with 26 additions and 6 deletions.
diff --git a/Bio/AlignIO/stockholm.pm b/Bio/AlignIO/stockholm.pm
@@ -337,9 +337,9 @@ our %WRITEMAP = (
 =head2 new
 
  Title   : new
- Usage   : my $alignio = Bio::AlignIO->new(-format => 'phylip'
+ Usage   : my $alignio = Bio::AlignIO->new(-format => 'stockholm'
 					  -file   => '>file');
- Function: Initialize a new L<Bio::AlignIO::phylip> reader or writer
+ Function: Initialize a new L<Bio::AlignIO::stockholm> reader or writer
  Returns : L<Bio::AlignIO> object
  Args    : -line_length :  length of the line for the alignment block
            -alphabet    :  symbol alphabet to set the sequences to.  If not set,

diff --git a/Bio/Restriction/Analysis.pm b/Bio/Restriction/Analysis.pm
@@ -520,9 +520,9 @@ sub fragment_maps {
     # for every enzyme this should cut down on the amount of
     # duplicated data we are trying to save in memory and make this
     # faster and easier for large sequences, e.g. genome analysis
-
+    
     my @cut_positions;
-    if (ref $enz eq '') {
+    if (ref $enz eq '' && exists $self->{'_cut_positions'}->{$enz}) {
         @cut_positions=@{$self->{'_cut_positions'}->{$enz}};
     } elsif ($enz->isa("Bio::Restriction::EnzymeI")) {
         @cut_positions=@{$self->{'_cut_positions'}->{$enz->name}};
@@ -531,7 +531,7 @@ sub fragment_maps {
         @cut_positions=@{$self->{'_cut_positions'}->{'multiple_digest'}};
     }
 
-    unless ($cut_positions[0]) {
+    unless (defined($cut_positions[0])) {
         # it doesn't cut
         # return the whole sequence
         # this should probably have the is_circular command
@@ -553,6 +553,7 @@ sub fragment_maps {
 
     my $start=1; my $stop; my %seq; my %stop;
     foreach $stop (@cuts) {
+        next if !$stop; # cuts at beginning of sequence
         $seq{$start}=$self->{'_seq'}->subseq($start, $stop);
         $stop{$start}=$stop;
         $start=$stop+1;

diff --git a/t/Restriction/Analysis.t b/t/Restriction/Analysis.t
@@ -8,7 +8,7 @@ BEGIN {
     use lib '.';
     use Bio::Root::Test;
 
-    test_begin(-tests => 177);
+    test_begin(-tests => 180);
 
     use_ok('Bio::Restriction::Enzyme');
     use_ok('Bio::Restriction::Enzyme::MultiCut');
@@ -292,3 +292,22 @@ eval {$re = Bio::Restriction::Enzyme->new(
 
 ok $@;
 like($@, qr(Unrecognized characters in site), 'bug 2139');
+
+# 0-pos bug (Elia Stupka)
+
+$seq = Bio::Seq->new(
+    -display_name   => 'foo',
+    -alphabet       => 'dna',
+    -seq            => 'GATCNNNNGATC'
+);
+
+$ra = Bio::Restriction::Analysis->new(-seq=>$seq);
+
+is $ra->fragments('HindIII'), 1, 'number of HindIII fragments';
+is $ra->fragments('BfuCI'), 2, 'number of EcoRI fragments';
+
+# passing a bad enzyme name
+
+is $ra->fragments('FooBarI'), 1, 'number of RsaI fragments';
+
+