[Bioperl-l] bp_genbank2gff.pl bug

Fields, Christopher J cjfields at illinois.edu
Thu Nov 10 14:17:57 EST 2011


This is running using an older version of bioperl (probably 1.6.0 or 1.6.1).  The warnings pop up when using perl v5.12 or v5.14; the first warning is from a bad tr/// in Bio::Range, the second is from bad usage of UNIVERSAL functions, both have ben addressed.

chris

On Nov 10, 2011, at 10:55 AM, Scott Cain wrote:

> Hi Angel,
> 
> Please keep correspondence on the mailing list.
> 
> I just ran bp_genbank2gff.pl with a genbank file (fruit fly mitocontria),
> and it worked fine.  I suspect there is something wrong with your genbank
> file.
> 
> Scott
> 
> 
> On Thu, Nov 10, 2011 at 3:15 AM, Angel Zaballos <azaballos at isciii.es> wrote:
> 
>> His Scott,
>> 
>> Thanks everyone for your help. I tried bp_genbank2gff3.pl, but the same
>> happened:
>> 
>> [root at localhost zaballos]# bp_genbank2gff3.pl babesiaChr3.gbk >
>> babesichr3_2.gff
>> Replacement list is longer than search list at
>> /usr/share/perl5/Bio/Range.pm line 251.
>> UNIVERSAL->import is deprecated and will be removed in a future perl at
>> /usr/share/perl5/Bio/Tree/TreeFunctionsI.pm line 94
>> 
>> However, the output file seems to be correct (Indeed, that was also the
>> case for  bp_genbank2gff.pl). I then ran ldHgGene and worked:
>> 
>> [zaballos at localhost ~]$ ./ldHgGene -out=babesiaChr3_2.gpe db tab
>> babesiachr3_2.gff
>> Reading babesiachr3_2.gff
>> Read 4776 transcripts in 8821 lines in 1 files
>>  4776 groups 1 seqs 1 sources 6 feature types
>> 2379 gene predictions
>> 
>> I'm using Fedora (for bioperl) and CentOS (for ldHgGene), virtualized on a
>> Mac with Parallels. Maybe tis is the cause for such a message.
>> 
>> Regards
>> 
>> 
>> Ángel
>> 
>> 
>> El 09/11/2011, a las 17:12, Scott Cain escribió:
>> 
>> Hi Angel,
>> 
>> I would suggest using bp_genbank2gff3.pl, as it is more actively
>> maintained; the bp_genbank2gff.pl script hasn't really been touched in
>> many years, and I imagine it's suffering from some serious code rot.
>> 
>> Scott
>> 
>> 
>> 2011/11/9 Angel Zaballos <azaballos at isciii.es>
>> 
>>> Running bp_genbank2gff.pl got this:
>>> 
>>> [root at localhost zaballos]# bp_genbank2gff.pl -stdout -accession
>>> AAXT01000001.1 > babesichr3.gff
>>> Replacement list is longer than search list at
>>> /usr/share/perl5/Bio/Range.pm line 251.
>>> 
>>> 
>>> 
>>> Ángel Zaballos
>>> Unidad de Genómica
>>> Centro Nacional de Microbiología-ISCIII
>>> Carretera Majadahonda-Pozuelo, Km 2,2
>>> 28220-Majadahonda
>>> 
>>> Tel: 918223994
>>> mail:  azaballos at isciii.es
>>> 
>>> 
>>> 
>>> 
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>> 
>> 
>> 
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> 
>> 
>> Ángel Zaballos
>> Unidad de Genómica
>> Centro Nacional de Microbiología-ISCIII
>> Carretera Majadahonda-Pozuelo, Km 2,2
>> 28220-Majadahonda
>> 
>> Tel: 918223994
>> mail:  azaballos at isciii.es
>> 
>> 
>> 
>> ************************* AVISO LEGAL *************************
>> Este mensaje electrónico está dirigido exclusivamente a sus destinatarios,
>> pudiendo contener documentos anexos de carácter privado y confidencial.
>> Si por error, ha recibido este mensaje y no se encuentra entre los
>> destinatarios, por favor, no use, informe, distribuya, imprima o copie su
>> contenido por ningún medio. Le rogamos lo comunique al remitente y borre
>> completamente el mensaje y sus anexos. El Instituto de Salud Carlos III no
>> asume ningún tipo de responsabilidad legal por el contenido de este mensaje
>> cuando no responda a las funciones atribuidas al remitente del mismo por la
>> normativa vigente.
>> 
>> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> 
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> Bioperl-l mailing list
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