[Bioperl-l] Please help me in using e-PCR parser module "Bio::Tools::EPCR"

Jason Stajich jason at bioperl.org
Wed Jul 2 04:00:08 UTC 2014

I am not sure I can help you at this time, but I would encourage you to use
the mailing list for assistance.
 There is nothing inherent in the tool for doing anything with exons but if
you want to print a feature in GFF format I would look at Bio::Tools::GFF
or Bio::FeatureIO (if that still works)

Another thing in this example is to change 'fasta' to 'genbank' for the
$seqout object so you can see the feature annotated in the sequence in
genbank format.

Jason Stajich
jason at bioperl.org

On Tue, Jul 1, 2014 at 12:18 PM, Firoz Ahmed <fa49 at nyu.edu> wrote:

>  Dear Prof. Jason E. Stajich,
>  I have a e-PCR output file on genomic sequence, and I want to extract
> the exon region between genomic position given in e-PCR output. Could you
> kindly tell me how can I use your program for this purpose.
>  Following are the commands and code I have used to test on example files
> provided with Bioperl, but the output is just sequence of
> "genomic-seq.fasta".
>  folder "BioPerl-1.6.923/t/data/
>                                                    genomic-seq.epcr
>                                                   genomic-seq.fasta
>  parser.pl
> ===============================================
>  #!/usr/bin/perl
>  # A simple annotation pipeline wrapper for ePCR data
>     # assuming ePCR data is already generated in file genomic-seq.epcr
>     # and sequence data is in fasta format in file called genomic-seq.fasta
>  use Bio::Tools::EPCR;
> use Bio::SeqIO;
> my $parser = Bio::Tools::EPCR->new(-file => 'genomic-seq.epcr');
> my $seqio = Bio::SeqIO->new(-format => 'fasta', -file =>
> 'genomic-seq.fasta');
> my $seq = $seqio->next_seq || die("cannot get a seq object from SeqIO");
>  while( my $feat = $parser->next_feature ) {
>         # add EPCR annotation to a sequence
>     $seq->add_SeqFeature($feat);
> }
> my $seqout = Bio::SeqIO->new(-format => 'fasta');
> $seqout->write_seq($seq);
>  ======================================================
> I use following command to run your script, both example files are in the
> working directory
>  ./parser.pl
>  Out put is fasta sequence from "genomic-seq.fasta".
>  Could you please tell me where I am doing wrong, and how can I also put
> the GFF3 file to get the the exon sequence?
>  Thanks a lot for your kind help.
> Firoz
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