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

[Warren W. Kretzschmar]

Where are you getting the filehandles from? That is, How are you
opening them? Can you show me the code?

Warren

On Thu, Jun 24, 2010 at 12:19 PM, Abhishek Pratap
<abhishek.vit at gmail.com> wrote:
> 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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>> >
>
>