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

[Dan Bolser]

Now logged here:
https://redmine.open-bio.org/issues/3206

And commented on here:
https://github.com/bioperl/bioperl-live/pull/7

Not sure how to provide pointers from those sources to this thread?


Cheers,
Dan.

On 28 March 2011 21:08, Dan Bolser <dan.bolser at gmail.com> wrote:
> On 27 March 2011 21:13, Chris Fields <cjfields at illinois.edu> wrote:
>> On Mar 27, 2011, at 12:55 PM, Dan Bolser wrote:
>>
>>> On 27 March 2011 18:28, Jason Stajich <jason at bioperl.org> wrote:
>>>> Dan - not sure why you would need to do this as length on an undef should
>>>> still return false (an undef).
>>>>
>>>> $ perl -e '$g=""; if( length($g)) { print "yes" } else { print "no"} print
>>>> "\n"'
>>>> no
>>>> $ perl -e '$g=undef; if( length($g)) { print "yes" } else { print "no"}
>>>> print "\n"'
>>>> no
>>>
>>> Doesn't the latter spew a warning? (The output before / after my 'bug
>>> fix' is the same, I just don't see 100s of warnings about undefined
>>> values).
>>
>> Only with later versions of perl (I think perl 5.12).
>>
>>>> Also, having no 'source' is probably not proper GFF3.
>>>
>>> I'm quite sure it is, but by GFF does have a source. I'm just calling
>>> 'features' with only a feature type and not a feature type and a
>>> source (because I only care about source). My call is pretty similar
>>> to the example here:
>>>
>>> http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/DB/SeqFeature/Store.pm#features
>>>
>>> @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');
>>
>> I think Jason is inferring that the GFF3 is invalid from your statement below re: $source_tag not being defined, which to me means the source attribute for the feature is not defined.
>>
>> Note: b/c something works with SF::Store does NOT mean the source is proper GFF3; it is quite possible to have invalid GFF3 loaded into the database w/o a hiccup.  I think the loader assumes the data loaded has already been validated; IIRC there is very little validation done on GFF3 loaded into SF::Store, particularly the 'type'.
>
> As I said, my GFF3 does have a source. I'll try to put together a test
> script, as it seems like the value should not be undef (but thanks for
> the tip Roy).
>
> I had a feeling that this relatively trivial fix was a sticking
> plaster on a larger problem.
>
>
>> chris
> Dan
>