[Bioperl-l] bp_genbank2gff.pl giving errors when using file....

Scott Cain scott at scottcain.net
Tue Jul 7 20:17:58 UTC 2009

Hi Gowthaman,

I thought I knew you but wasn't sure; hi again.

About the problematic genbank files: was it something that the genbank  
parser should have handled but did not?  If so, we should get that  
fixed anyway.


On Jul 7, 2009, at 4:06 PM, Gowthaman Ramasamy wrote:

> Hi Scott,
> Thanks for the mail. Its funny. Knowing you (at GMOD meeting) I  
> wouldn't
> mistake it in any other ways.
> I was rushing back to email the list to tell I got it working. There  
> is
> NOTHING wrong with script. Its perfectly good. (not many scripts  
> stands the
> time. This one does).
> Its the genbank record. Some of the genbank records I tried did  
> produce that
> error, while others did not. I'll dig into those files to see if  
> anything is
> obvious (to my eyes) that causes this error.
> PS1: I tried changing the name, and that did NOT solve the problem.
> Thanks once again,
> Gowtham
> On 7/7/09 12:18 PM, "Scott Cain" <cain.cshl at gmail.com> wrote:
>> Hi Gotham,
>> I was going to send you an email to complain to the author, until I
>> realized that it was me :-)
>> It has been quite a while since I looked at the code for this script,
>> as the one I typically use these days is bp_genbank2gff3.pl, but I
>> think I have a "fix".  Try changing the name of the file to
>> NC_004329.gb or .gbk or .genbank.  That is the (very weak) heuristic
>> that the script uses to determine if a file is genbank formated  
>> versus
>> embl (note that the error message says it's not an embl file--that's
>> why).  If that doesn't do it, let me (and the mailing list) know.
>> Scott
>> PS: I wasn't really going to say to complain to the author directly--
>> that was just me trying to be funny.
>> PPS: As another side note, it is fairly funny to me that the code  
>> that
>> this script depends upon, Bio::DB::GFF::Adaptor::biofetch, says in  
>> the
>> documentation that it is proof-of-principle and should not be used in
>> production.
>> On Jul 7, 2009, at 1:59 PM, Gowthaman Ramasamy wrote:
>>> Hi All,
>>> I am trying to  use bp_genbank2gff.pl script to convert a locally
>>> downloaded genbank file. It is throwing stack errors. But, the
>>> script works beautifully when I use --accession option to download
>>> and convert.
>>> Any suggestions? Thanks very much for checking this.
>>> the command i use:
>>> perl bp_genbank2gff.pl --stdout --file NC_004329.nb
>>> and i am getting the following exception message:
>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>> MSG: EMBL stream with no ID. Not embl in my book
>>> STACK: Error::throw
>>> STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.5/Bio/
>>> Root/Root.pm:359
>>> STACK: Bio::SeqIO::embl::next_seq /usr/lib/perl5/site_perl/5.8.5/ 
>>> Bio/
>>> SeqIO/embl.pm:189
>>> STACK: Bio::DB::GFF::Adaptor::biofetch::load_from_file /usr/lib64/
>>> perl5/site_perl/5.8.5/x86_64-linux-thread-multi/Bio/DB/GFF/Adaptor/
>>> biofetch.pm:163
>>> STACK: bp_genbank2gff.pl:274
>>> -----------------------------------------------------------
>>> Many thanks in advance,
>>> Gowtham
>>> _______________________________________________
>>> 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

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