[Bioperl-l] fasta2gff_landmark ...

Dan Bolser dan.bolser at gmail.com
Thu May 14 04:16:33 EDT 2009

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,

> Scott

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