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

[Abhishek Pratap]

Thanks everyone for your input. I have the script working.

Chris : Not sure what is the rationale, write_seq and next_seq has different
key names in the hash ref( eg . 'display_id' and '-id') . This could
possibly cause conflicts in future development. Also just wondering why
currently only Bio:SeqIO:Quality object works with write_seq.

-Abhi

On Thu, Jun 24, 2010 at 2:14 PM, Chris Fields <cjfields at illinois.edu> wrote:

> The best way to get that is by using next_seq(), not next_dataset.  It will
> not be as fast, but should suffice.
>
> At the moment we don't have plans on supporting output for hash refs frm
> next_dataset until we can standardize upon a way for describing such data
> from various parsers.
>
> chris
>
> On Jun 24, 2010, at 1:09 PM, Abhishek Pratap wrote:
>
> > Dear Chris
> >
> > I am indeed passing hash ref via next_dataset. Any slick way to convert
> the ref to Bio::Seq::Quality format.
> >
> > Thanks!
> > -Abhi
> >
> > On Thu, Jun 24, 2010 at 1:19 PM, Chris Fields <cjfields at illinois.edu>
> wrote:
> > The error message is pretty straightforward.  What are you passing into
> write_seq?  Is it a simple hash-ref (maybe via next_dataset)?  write_seq()
> only supports Bio::Seq::Quality.
> >
> > chris
> >
> > On Jun 24, 2010, at 12:03 PM, Abhishek Pratap wrote:
> >
> > > After a bit more error checking, I was able to resolve the previous
> error
> > >
> > > Resolved 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.
> > > This happened due to null value returned by one of the hash.
> > >
> > > However I am hitting a new issue.
> > > New Error : Can't call method "isa" on unblessed reference at
> > > /local/projects/grc/devel/packages/bioperl-live/Bio/SeqIO/fastq.pmline 126,
> > > <GEN12> line 49
> > >
> > >
> > > -A
> > >
> > >
> > >
> > > On Thu, Jun 24, 2010 at 12:55 PM, Abhishek Pratap <
> abhishek.vit at gmail.com>wrote:
> > >
> > >> 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;
> > >>>>>>>> }
> > >>>>>>>> }
> > >>>>>>>> _______________________________________________
> > >>>>>>>> Bioperl-l mailing list
> > >>>>>>>> Bioperl-l at lists.open-bio.org
> > >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > >>>>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>
> > >>>> _______________________________________________
> > >>>> Bioperl-l mailing list
> > >>>> Bioperl-l at lists.open-bio.org
> > >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > >>>
> > >>>
> > >>
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
>