[Bioperl-l] Use of uninitialized value in length at Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1062

[Dan Bolser]

Hi all,

I'm not sure why, but the code in Bio/DB/SeqFeature/Store/DBI/mysql.pm uses:
    if (length $source_tag) {

within the '_types_sql' function to test if $source_tag is defined
(and has a length). This obviously fails when $source_tag it isn't
defined, and I see the above error message from my script when I call
the 'features' function (as shown below).

>From tests (thanks to rbuels in #bioperl) it seems the value of $type
is simply 'fwd link intensity', so:
      ($primary_tag,$source_tag) = split ':',$type,2;

on line 1047 leaves $source_tag undefined.

Here is my proposed fix:

diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Sto
index 00103c2..dfc70c0 100644
--- a/Bio/DB/SeqFeature/Store/DBI/mysql.pm
+++ b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
@@ -1057,8 +1057,8 @@ sub _types_sql {
       ($primary_tag,$source_tag) = split ':',$type,2;
     }

-    if (length $source_tag) {
-      if (length($primary_tag)) {
+    if (defined $source_tag && length $source_tag) {
+      if (defined $primary_tag && length($primary_tag)) {
         push @matches,"tl.tag=?";
         push @args,"$primary_tag:$source_tag";
       }


which seems to work. I'd write some tests, but an old bug that I can't
track down prevents me from running tests on this package
(http://bugzilla.open-bio.org/show_bug.cgi?id=2899).

Cheers,
Dan.


Here are some snippets of code to give context:

my $intensities = Bio::DB::SeqFeature::Store->
  new( -adaptor => 'DBI::mysql',
	-dsn => 'db:mysql.server.ac.uk',
	-user => 'me',
	-pass => 'secret',
       -verbose => $verbose,
     );

my @fwd_intensity = $intensities->
    features( -seqid => 'some-id', -type => 'fwd link intensity',
              -start => 10,
              -end   => 200,
    );