[Bioperl-l] bp_genbank2gff3.pl error on last line ("//")
Chris Fields
cjfields at illinois.edu
Sun Jul 25 19:20:09 UTC 2010
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.
>
>
>
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