[Bioperl-l] Genbank to gff3 conversion problem

Smithies, Russell Russell.Smithies at agresearch.co.nz
Thu Jan 29 16:55:30 EST 2009


Do you still have problems if you try to parse the complete record rather than that pesky version with contig joins?
Eg http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=37558541&view=gbwithparts


--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Chris Mungall
> Sent: Friday, 30 January 2009 10:27 a.m.
> To: shafeeq rim
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Genbank to gff3 conversion problem
> 
> 
> This looks like a problem with the Unflattener code (which I wrote a
> while ago) - as ChrisF states, this is sometimes required to
> reconstruct the hierarchical subfeature relations from the 'flat'
> genbank model
> 
> Here is  NT_011512:
> 
> http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&val=37558541
> 
> It's human chromosome 21
> 
> This genbank record that is split over multiple sub-records, using
> join directives to stitch it all back together. I once new how to
> handle such beasts in bioperl, but I think I've forgotten. In any
> case, the unflattener does not make any attempt to download and join
> together the sequence fragments, it just gets confused by this record
> and throws a wobbly.
> 
> A bioperl guru may be able to help with the correct strategy here, but
> roughly speaking I can see two alternate approaches:
> 
> 1. reconstruct the entire chromosome record and feed that to the
> unflattener
> 2. iterate though each record running the gb2gff conversion on each,
> then stitch the gff records together
> 
> 2 will be quite tricky because of the coordinate transformation. On
> the other hand, there may be memory issues.
> 
> I'm sure this is doable as I used to regularly load all of genbank
> human into a bioSQL database using a predecessor of the unflattener;
> I'm just not sure what the best strategy is these days. I have a
> feeling the human assemblies are (or were) available on a one file per
> chromosome basis from the NCBI ftp site. This may be your best bet.
> 
> On Jan 28, 2009, at 8:23 PM, shafeeq rim wrote:
> 
> > Hi,
> >
> > I was trying my hands on  bp_genbank2gff3.pl script
> > in Bioperl but getting lots of errors. I first tried with .gbk file
> in
> > genbank and then .gbs file but still no success. I actually want
> Human
> > genome annotation file in gff3 format for my application. Is there
> > any other
> > software or script for gff3 conversion from genbank format apart from
> > this bioperl script? Readseq utility is there but it converts only
> > into
> > gff2.
> > I extracted and removed problematic file but still of no use
> > NT_011512.
> >
> > I am getting errors like this :-
> > I am using this command perl bp_genbank2gff3.pl ref_chr21.gbk
> > ##########################################################
> > STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/
> > share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549
> > STACK (eval) bp_genbank2gff3.pl:378
> > STACK main::unflatten_seq bp_genbank2gff3.pl:377
> > STACK toplevel bp_genbank2gff3.pl:229
> >
> > --------------------------------------
> >
> > Possible gene unflattening error withNT_011512: consult STDERR
> >
> > ------------- EXCEPTION  -------------
> > MSG: seq_id must be set
> > STACK
> Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id
> > /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242
> > STACK main::generic_features bp_genbank2gff3.pl:353
> > STACK toplevel bp_genbank2gff3.pl:254
> > #####################################################
> >
> > Thanks in advance
> > Regards
> > Shafeeq
> >
> >
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> http://messenger.yahoo.com/invite/
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> >
> 
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