Merge branch 'master' into json-stabilize

GMOD · Feb 7, 2012 · 2ba41ea · 2ba41ea
2 parents c2d3c60 + 66c055d
commit 2ba41ea
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Showing 3 changed files with 5 additions and 2 deletions.
diff --git a/docs/tutorial/data_files/volvox.fa b/docs/tutorial/data_files/volvox.fa
@@ -833,3 +833,6 @@ tgaactcgtcacgtcatgcctagctcccggttgaaacacgaagacgcgtgaacctatctt
 tgcttactattcgcctcctttaagaggcttcttgatgtggctctgcgacatggacagtag
 tagttgtacctgggtatgttagtgaaattacaagtacctcaaaaacgaattacgtgtata
 gagattatgtcactccgtcac
+>ctgB
+ACTGATCGATGATGACTGACTAGTAGA
+ACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGC
diff --git a/lib/FastaDatabase.pm b/lib/FastaDatabase.pm
@@ -67,7 +67,7 @@ sub from_fasta {
         local $/ = "\n>";
         while( my $entry = <$fh> ) {
 	    my ( $name, $seq ) = split "\n", $entry, 2;
-	    ($name) = $name =~ /^\s*>\s*(\S+)/;
+	    ($name) = $name =~ /^\s*>?\s*(\S+)/;
             $seq =~ s/\s//g;
             $seqdata->{$name} = $seq;
         }

diff --git a/tests/perl_tests/FastaDatabase.t b/tests/perl_tests/FastaDatabase.t
@@ -9,7 +9,7 @@ use FastaDatabase;
 my $db = FastaDatabase->from_fasta( 'sample_data/raw/volvox/volvox.fa', glob 'sample_data/raw/yeast_scaffolds/chr*.fa.*' );
 my $seq_ids = [ sort $db->seq_ids ];
 is_deeply( $seq_ids,
-           [ sort 'chrI','chrII', 'ctgA' ],
+           [ sort 'chrI','chrII', 'ctgA', 'ctgB' ],
            'got right seq ids from FastaDatabase with multiple fasta files, some compressed, some not'
          )
   or diag explain $seq_ids;