[Bioperl-l] reading gz fastq File

[Roy Chaudhuri]

Hi Shalu,

Yes, I can replicate this error with bioperl 1.7.1, but 1.6.923 works as 
expected. I think it's a bug since the docs suggest that it should work.

As a workaround you can use:

open my $fh, "gunzip -c $ARGV[0]|" or die $!;
my $in=Bio::SeqIO->new(-fh=>$fh, -format=>'fastq');

Cheers,
Roy.

On 25/02/2019 16:00, shalu sharma wrote:
> Hi Everyone,
>      So i am trying to work on gzip fastq files. In past my script used 
> to work fine. Now when i ran the same script it gives me an error.
> I am just pasting few lines for example and an error message.
> Would really appreciate your help.
> 
> use Bio::SeqIO;
> 
> use Bio::Seq::Quality;
> 
> $in = Bio::SeqIO->new(-file => "gunzip -c $ARGV[0]|", -format => 'fastq');
> 
> while(my $seq = $in->next_seq){
> 
> my $id = $seq->id;
> 
> print "$id\n";
> 
> }
> 
> 
> Error message:
> 
> MSG: Could not read file 'gunzip -c com.fastq.gz|': No such file or 
> directory
> 
> STACK: Error::throw
> 
> STACK: Bio::Root::Root::throw 
> /usr/local/apps/eb/BioPerl/1.7.1-foss-2016b-Perl-5.24.1/lib/perl5/site_perl/5.24.1/Bio/Root/Root.pm:447
> 
> STACK: Bio::Root::IO::_initialize_io 
> /usr/local/apps/eb/BioPerl/1.7.1-foss-2016b-Perl-5.24.1/lib/perl5/site_perl/5.24.1/Bio/Root/IO.pm:268
> 
> STACK: Bio::SeqIO::_initialize 
> /usr/local/apps/eb/BioPerl/1.7.1-foss-2016b-Perl-5.24.1/lib/perl5/site_perl/5.24.1/Bio/SeqIO.pm:513
> 
> STACK: Bio::SeqIO::fastq::_initialize 
> /usr/local/apps/eb/BioPerl/1.7.1-foss-2016b-Perl-5.24.1/lib/perl5/site_perl/5.24.1/Bio/SeqIO/fastq.pm:30 
> <http://fastq.pm:30>
> 
> STACK: Bio::SeqIO::new 
> /usr/local/apps/eb/BioPerl/1.7.1-foss-2016b-Perl-5.24.1/lib/perl5/site_perl/5.24.1/Bio/SeqIO.pm:389
> 
> STACK: Bio::SeqIO::new 
> /usr/local/apps/eb/BioPerl/1.7.1-foss-2016b-Perl-5.24.1/lib/perl5/site_perl/5.24.1/Bio/SeqIO.pm:435
> 
> STACK: testGZ.pl:5
> 
> 
> Thanks
> 
> Shalu
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>