[Bioperl-l] Passing/Storing "Bio::SeqIO" object to a function

[Abhishek Pratap]

Dear Warren

Thanks for your quick reply.  I am doing something very close to what you
have suggested but I see errors which might be due to some silly mistake I
am making. The difference is instead of array I am using a hash to help me
extract file names by key value later.

I am writing data like this.

my $file_handle = $bins{$bin_name};
 $file_handle->write_seq($data);

Gives me an error
Can't call method "write_seq" on an undefined value at
/home/apratap/dev/eclipse_workspace/Illumina/demultiplex_GA_data.pl line
139, <GEN12> line 5.

-Abhi

On Thu, Jun 24, 2010 at 11:24 AM, Warren W. Kretzschmar <wkretzsch at gmail.com
> wrote:

> Hi,
> My understanding is that you are using a SeqIO object in order to
> create correctly parsed output files.
>
> In that case for each SeqIO object, open it like this:
>
> for (0..9){
> $file = "my_file_$_";
> push @outseqIOs, Bio::SeqIO->new(-file   => ">$file", -format => $format );
> }
>
> simply make $file correspond to the file (or bin) you want to put your
> data into.
>
> then pass @outseqIOs to your other subroutine and once you've created
> a seq object, write it to the bin you want it to go to (in this case
> file number "7"):
>
> $outseqIOs[7]->write_seq($seq);
>
> I haven't tested the code, but that's the kind of thing I think you're
> looking for. For more info, look at the howto:
> http://www.bioperl.org/wiki/HOWTO:SeqIO
>
> Warren
>
> On Thu, Jun 24, 2010 at 10:20 AM, Abhishek Pratap
> <abhishek.vit at gmail.com> wrote:
> > Hi All
> >
> > I may be hitting a problem which probably hints at my grip of the
> language.
> > I am trying to store Bio::SeqIO object in a hash. I have creates couple
> of
> > Bio::SeqIO objects in a method and storing them as a hash reference. The
> > goal is to use them in another subroutine for writing out data to each
> file.
> > The script is trying to bin data into different files.
> >
> >
> > Any idea how I could achieve creating file handles  thru "Bio::SeqIO"
> object
> > in one routine and pass them to another for writing.
> >
> >
> > Thanks!
> > -Abhi
> >
> > foreach my $bin (keys %{ $indexes->{$lane} })
> >  {
> > my $sample_name = $indexes->{$lane}->{$bin}->{'sample'};
> >  my $path="$outpath".'/'."$sample_name";
> > mkpath( $path, { verbose => 1, mode => 0711 });
> >        my $out = Bio::SeqIO->new(-format=>'fastq-illumina', -file =>
> > ">$outpath/$sample_name/$fastQFile");
> > $indexes->{$lane}->{$bin}->{'file_handle'}=$out;
> >  }
> > }
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> >
>