[Bioperl-l] bp_genbank2gff3.pl error on last line ("//")

David Breimann david.breimann at gmail.com
Sun Jul 25 15:52:53 EDT 2010


Thank you guys. I'm quite new to all this github stuff, so in order to view
to use to updated version should I first update my clone of bioperl-live
(git pull?) then go through the whole build and install again?

Second, I have just noticed that bp_genbank2gff3.pl returns an error when
given a circular genome with a feature that spans the "end" of the genome
(e.g., assume the genome size is 1000np and a feature spans
join(900..1000,1..100).

Finally, is it possible to tell bp_genbank2gff3.pl to extract the features
only (no sequences)? Currently I use the -y flag then delete the fasta file.

Thanks!


On Sun, Jul 25, 2010 at 10:20 PM, Chris Fields <cjfields at illinois.edu>wrote:

> Pull request was merged into master branch of bioperl-live.  Thanks!
>
> Oddly, pull requests aren't coming through via the mail list, I'll look
> into the issue.
>
> chris
>
> On Jul 25, 2010, at 1:58 PM, John Anderson wrote:
>
> >
> > On Jul 25, 2010, at 8:17 AM, David Breimann wrote:
> >
> >> I'm using bp_genbank2gff3.pl and seems to work fine, but when I use
> >> the -y (split) option it always gives an error on the very last line
> >> of the genbank, whch is actually "//":
> >>
> >> For example,
> >>
> >>   Can't use an undefined value as a symbol reference at
> >> /usr/local/bin/bp_genbank2gff3.pl line 660, <FH> line 41443.
> >>
> >> What's the problem?
> >>
> >
> > I filed a bug for you; it's #3124 and can be seen at <
> http://bugzilla.open-bio.org/show_bug.cgi?id=3124>
> >
> > The following patch fixes it for me; it can be found in <
> http://github.com/genehack/bioperl-live/tree/topic/bug-3124>. I've sent a
> pull request for this change.
> >
> >> diff --git a/scripts/Bio-DB-GFF/genbank2gff3.PLS
> b/scripts/Bio-DB-GFF/genbank2gff3.PLS
> >> index 1216810..6bdae9d 100755
> >> --- a/scripts/Bio-DB-GFF/genbank2gff3.PLS
> >> +++ b/scripts/Bio-DB-GFF/genbank2gff3.PLS
> >> @@ -654,7 +654,7 @@ for my $file ( @files ) {
> >>     }
> >>
> >>      ## FIXME for piped output w/ split FA files ...
> >> -    close($lumpfa_fh);
> >> +    close($lumpfa_fh) if $lumpfa_fh;
> >>     if (!$split && $outfa && $lump_fh) {
> >>       print $lump_fh "##FASTA\n"; # GFF3 spec
> >>       open $lumpfa_fh, $outfa or warn "reading FA $outfa: $!";
> >>
> >>
> >
> > chrs,
> > john.
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


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