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

Thu Jun 24 18:14:41 UTC 2010

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.pm line 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;
> >>>>>>>> }
> >>>>>>>> }
> >>>>>>>> _______________________________________________
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> >>>>>>>> Bioperl-l at lists.open-bio.org
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> >>>>>>>>
> >>>>>>
> >>>>>>
> >>>>>
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> >>>
> >>>
> >>
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> 