[Bioperl-l] pls help..

Scott Cain scott at scottcain.net
Fri Aug 19 10:38:16 EDT 2011


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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