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

John Anderson genehack at genehack.org
Sun Jul 25 14:58:33 EDT 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.





More information about the Bioperl-l mailing list