[Bioperl-l] pls help..

Chris Fields cjfields at illinois.edu
Fri Aug 19 10:26:06 EDT 2011


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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