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

[Abhishek Pratap]

Hi Chris

Thanks for joining this conversation. I dont think max limit of file handles
is a problem. I am opening about 12 in this case.

[apratap at grima]$ ulimit -n
4096

-A


On Thu, Jun 24, 2010 at 12:52 PM, Chris Fields <cjfields at illinois.edu>wrote:

> Are you sure you haven't hit the max limit for open filehandles for your
> OS?  Attempting to open a filehandle when you exceed this limit simply
> returns undef, which might explain the error.  On my Mac:
>
> cjfields4:~ cjfields$ ulimit -n
> 256
>
> On my ubuntu box:
>
> cjfields at pyrimidine:~$ ulimit -n
> 1024
>
> I think Windows used to be much less, not sure now.  You might not be able
> to reset this on some systems.
>
> chris
>
> On Jun 24, 2010, at 11:26 AM, Abhishek Pratap wrote:
>
> > Sure. Here is the full subroutine where I am opening the file handle and
> > storing them
> >
> > Thanks for your help,
> > -A
> >
> > sub createBins {
> > my $SUB ='createBins';
> > my $PWD = `pwd`;
> > my $outpath = shift @_;
> > my $lane = shift @_ ;
> >
> > 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");
> > $bins{$bin}=$out;
> > }
> > }
> >
> >
> > On Thu, Jun 24, 2010 at 12:22 PM, Warren W. Kretzschmar <
> wkretzsch at gmail.com
> >> wrote:
> >
> >> 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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> >>>>> Bioperl-l at lists.open-bio.org
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> >>>>>
> >>>
> >>>
> >>
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