[Bioperl-l] pls help..

Scott Cain scott at scottcain.net
Mon Aug 22 11:51:55 EDT 2011


Hello Ravi,

Please keep the BioPerl mailing list cc'ed.

I downloaded your 1.7GB multi-genbank file and started processing it
with bp_genbank2gff3.pl and I killed it when the GFF file got to 10GB,
however, it was working as expected.  I suggest you upgrade to the
most recent release of BioPerl and try again.  Additionally, it might
make sense to break that big multi-genbank file into smaller files.

Scott


On Sun, Aug 21, 2011 at 11:33 AM, Ravi Devani <ravi.devani89 at gmail.com> wrote:
> scott i hv given the link to the gbk file, please kindly help me
>
> On 8/19/11, Scott Cain <scott at scottcain.net> wrote:
>> Ravi,
>>
>> I also meant to ask what version of BioPerl you are using.  When I run
>> this command
>>
>>   bp_genbank2gff3.pl NW_002121371.gbk
>>
>> I get a rather dull GFF3 file with 4 lines of GFF (one region and
>> three gaps) and a fasta section.
>>
>> Scott
>>
>>
>> On Fri, Aug 19, 2011 at 12:33 PM, Ravi Devani <ravi.devani89 at gmail.com>
>> wrote:
>>> No the genbank file has not been manipulated
>>>
>>> On 8/19/11, Scott Cain <scott at scottcain.net> 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>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain
>>>> dot
>>>> net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>>
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot
>> net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>



-- 
------------------------------------------------------------------------
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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