[Bioperl-l] possible bug in Bio::SeqIO::fastq

Chris Fields cjfields at illinois.edu
Tue Oct 12 10:50:30 EDT 2010


Albert, 

Have you tried bioperl-live?  This is already fixed there.

chris

On Oct 12, 2010, at 7:34 AM, Albert Vilella wrote:

> Hi,
> 
> I found what seems to me could be a bug in the fastq module, which is
> that if the
> last line of the raw_quality section is a single "0" character, a
> "if($line)" isn't
> returning it properly, because it should be "if(defined $line)" instead.
> 
> Find here a test case and the line in question:
> 
> ----
> use strict;
> use Bio::SeqIO;
> 
> my $consio = Bio::SeqIO->new
>  (-format => 'fastq',
>   -fh => \*DATA);
> 
> my $onelineconsout = Bio::SeqIO->new
>  (-format => 'fastq',
>   -fh => \*STDOUT);
> 
> while (my $seq = $consio->next_seq) {
>  next if ($seq->seq =~ /^n+$/);
>  $seq->seq(uc($seq->seq));
>  $onelineconsout->write_seq($seq);
> }
> $consio->close;
> $onelineconsout->close;
> 
> __DATA__
> @SRR031652.634472
> agtgcgctgatctgtggcccgtattgcctcaacgcaagctcaatagcttgagtatattaa
> a
> +
> 01111111111111100111111--,,011111101111111110111111111111110
> 0
> ----
> 
> --- /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm
> 2010-10-12 13:26:06.491743000 +0100
> +++ /homes/avilella/src/BioPerl-1.6.1/Bio/SeqIO/fastq.pm~
> 2010-10-12 13:07:27.462833000 +0100
> @@ -80,7 +80,7 @@
>                 last FASTQ
>             }
>             chomp $line;
> -            if (!defined($line)) {
> +            if (!$line) {
>                 delete $self->{lastline};
>                 last FASTQ;
>             }
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