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

[Scott Cain]

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
>
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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