Re: Please help me in using e-PCR parser module "Bio::Tools::EPCR"

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Re: Please help me in using e-PCR parser module "Bio::Tools::EPCR"

Jason Stajich-3
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.




On Tue, Jul 1, 2014 at 12:18 PM, Firoz Ahmed <[hidden email]> 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

===============================================
#!/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


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
NYU, USA


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