[Bioperl-l] pls help..

Scott Cain scott at scottcain.net
Mon Aug 29 14:34:41 EDT 2011


Hi Ravi,

Sorry I took a while to get back to you; I was on vacation last week.
Also, please keep correspondence on the bioperl mailing list.  If you
had, perhaps somebody else would have provided another answer by now.

I found the bug in the genbank2gff3 script that causes this problem.
You have a few options for how to proceed:

1.  Split the multi-genbank file into individual files, put them in a
directory, and point the script at that directory (with the --dir
flag).  If you do this, you won't have to do anything with your
BioPerl installation.

2. Get a fresh checkout of bioperl-live from git and install BioPerl
from it, as I just committed the fix to the master branch.

3. Manually apply the fix that I just put into master.  The diff is here:

  https://github.com/bioperl/bioperl-live/commit/1cff7d541e704a1f35d85bb27a0ab5911d89f8df

Scott


On Tue, Aug 23, 2011 at 12:55 AM, Ravi Devani <ravi.devani89 at gmail.com> wrote:
> Yes the script works but have you seen the gff file generated by it. It has
> multiple entries for the same features. And the file keeps on growing in
> size with thw same features repeated many times. Thats the problem..
>
> Thanking you,
> Ravi
>
>
>
>



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