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

[Chris Fields]

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;
>>>>> }
>>>>> }
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>> 
>>> 
>>> 
>> 
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