[Bioperl-l] pls help..

Chris Fields cjfields at illinois.edu
Fri Aug 19 15:19:40 EDT 2011


Yeah, the output is rather odd.  Maybe it's using the contig file version?

chris

On Aug 19, 2011, at 9:38 AM, Scott Cain wrote:

> I was wondering if perhaps the genbank file had been manipulated in some way.
> 
> Scott
> 
> 
> On Fri, Aug 19, 2011 at 10:26 AM, Chris Fields <cjfields at illinois.edu> wrote:
>> Scott,
>> 
>> http://www.ncbi.nlm.nih.gov/nuccore/NW_002121371.1?report=gbwithparts&log$=seqview
>> 
>> (it's in the GFF file)
>> 
>> It definitely is getting stuck in a loop for the genomic region, but using the file for GFF3 doesn't make sense (very few features of note).
>> 
>> On Aug 19, 2011, at 8:45 AM, Scott Cain wrote:
>> 
>>> Ravi,
>>> 
>>> The gff file is fairly useless from a debugging perspective. Can you please attach the genbank file you're using?  Also, please indicate what version of bioperl you're using.
>>> 
>>> Scott
>>> 
>>> 
>>> Sent from my iPhone
>>> 
>>> On Aug 19, 2011, at 1:16 AM, Ravi Devani <ravi.devani89 at gmail.com> wrote:
>>> 
>>>> ---------- Forwarded message ----------
>>>> From: Ravi Devani <ravi.devani89 at gmail.com>
>>>> Date: Thu, Aug 18, 2011 at 12:40 PM
>>>> Subject: pls help..
>>>> To: scott at scottcain.net
>>>> 
>>>> 
>>>> i tried to create a gff3 file from .gbk file using bp_genbank2gff3.pl but
>>>> what i get is same features repeating many times.. and the file keeps
>>>> growing in size ntil my harddisk gets full.. i have tried to filter all
>>>> other features except "region" but still it repeats a single entry many
>>>> times..  i have attached a part of the file generated.. pls kindly help me.
>>>> <ref_chrUn.gff>
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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




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