[Bioperl-l] fasta2gff_landmark ...

[Scott Cain]

Hi Dan

Could the uninit warnings be a data problem?  Like something as simple
as having a space betwen the carrot and the id?

Scott


On Thursday, May 14, 2009, Dan Bolser <dan.bolser at gmail.com> wrote:
> 2009/5/13 Scott Cain <scott at scottcain.net>:
>> Hi Dan,
>>
>> I've already done this; take a look at:
>>
>> http://gmod.cvs.sourceforge.net/viewvc/*checkout*/gmod/schema/chado/bin/gmod_fasta2gff3.pl
>>
>> While it is part of the GMOD/Chado distribution, the only modules it
>> uses is Bio::DB::Fasta and GetOpt::Long, and it has some nice
>> convenience functions for modifying the resulting GFF.
>
> Thanks Scott,
>
> That is more or less exactly what I need (and a vote for 'wait for the
> code audit' I guess ;-).
>
>
> I'm still seeing a couple of errors:
>
> Use of uninitialized value in pattern match (m//) at
> ~/perl5/lib/perl5/Bio/DB/Fasta.pm line 1168.
> Use of uninitialized value in exists at
> ~/perl5/lib/perl5/Bio/DB/Fasta.pm line 617.
>
>
> But the resulting GFF looks fine.
>
> Thanks again,
> Dan.
>
>
>> Scott
>>
>

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research