Bio::SeqIO::embl::_write_id_line: accession_number() returns 'unknown…

…' for unassigned accession# Signed-off-by: Kai Blin <kai.blin@biotech.uni-tuebingen.de>
bioperl · Nov 7, 2011 · 5e552c0 · kblin · Nov 10, 2011 · cjfields
1 parent d447967
commit 5e552c0
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Showing 2 changed files with 15 additions and 2 deletions.
diff --git a/Bio/SeqIO/embl.pm b/Bio/SeqIO/embl.pm
@@ -505,7 +505,7 @@ sub _write_ID_line {
 
         # The sequence name is supposed to be the primary accession number,
         my $name = $seq->accession_number();
-        if (!$name) {
+        if (!defined($name) || $name eq 'unknown') {
             # but if it is not present, use the sequence ID.
             $name = $seq->id();
         }

diff --git a/t/SeqIO/embl.t b/t/SeqIO/embl.t
@@ -8,7 +8,7 @@ BEGIN {
 	use lib '../..';
 	use Bio::Root::Test;
 
-	test_begin(-tests => 95);
+	test_begin(-tests => 96);
 
     use_ok('Bio::SeqIO::embl');
 }
@@ -315,3 +315,16 @@ foreach my $feature ($seq->top_SeqFeatures) {
     is($embl_species->ncbi_taxid, 9606, "The taxid of the source feature overrides that of the OX line");
     is($embl_species->binomial(), 'Anopheles gambiae', "Name has roundtripped");
 }
+
+# Handle Seq objects that only define an ID, not an accession number
+{
+    my $seq = Bio::Seq->new(-seq=>'actg', -id=>'test_id');
+
+    my $string;
+    open(my $str_fh, '>', \$string) || skip("Can't open string, skipping", 1);
+
+    my $out = Bio::SeqIO->new(-format=>'embl', -fh=>$str_fh);
+    $out->write_seq($seq);
+
+    ok($string =~ m/ID   test_id;/, "The ID field was written correctly");
+}