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

Chris Fields cjfields at illinois.edu
Sun Jul 25 15:20:09 EDT 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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