[Bioperl-l] bp_genbank2gff3.pl error on last line ("//")
John Anderson
genehack at genehack.org
Sun Jul 25 18:58:33 UTC 2010
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.
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