<div dir="ltr">I am not sure I can help you at this time, but I would encourage you to use the mailing list for assistance.<div> 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)</div>
<div><br></div><div>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.<br><div><br><div class="gmail_extra">
<br clear="all"><div><div dir="ltr">Jason Stajich<br><a href="mailto:jason@bioperl.org" target="_blank">jason@bioperl.org</a><br><a href="http://bioperl.org/wiki/User:Jason" target="_blank">http://bioperl.org/wiki/User:Jason</a><br>
<a href="http://twitter.com/hyphaltip" target="_blank">http://twitter.com/hyphaltip</a></div></div>
<br><br><div class="gmail_quote">On Tue, Jul 1, 2014 at 12:18 PM, Firoz Ahmed <span dir="ltr"><<a href="mailto:fa49@nyu.edu" target="_blank">fa49@nyu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
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<div>Dear Prof. Jason E. Stajich,</div>
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<div>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.</div>
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<div>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". </div>
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<div>folder "BioPerl-1.6.923/t/data/<br>
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genomic-seq.epcr<br>
<div> genomic-seq.fasta<br>
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<div><a href="http://parser.pl" target="_blank">parser.pl</a> </div>
<div>===============================================</div>
<div>
<div>#!/usr/bin/perl</div>
<div> # A simple annotation pipeline wrapper for ePCR data</div>
<div> # assuming ePCR data is already generated in file genomic-seq.epcr</div>
<div> # and sequence data is in fasta format in file called genomic-seq.fasta</div>
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<div>use Bio::Tools::EPCR;</div>
<div>use Bio::SeqIO;</div>
<div>my $parser = Bio::Tools::EPCR->new(-file => 'genomic-seq.epcr');</div>
<div>my $seqio = Bio::SeqIO->new(-format => 'fasta', -file => 'genomic-seq.fasta');</div>
<div>my $seq = $seqio->next_seq || die("cannot get a seq object from SeqIO");</div>
<div><br>
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<div>while( my $feat = $parser->next_feature ) {</div>
<div> # add EPCR annotation to a sequence</div>
<div> $seq->add_SeqFeature($feat);</div>
<div>}</div>
<div>my $seqout = Bio::SeqIO->new(-format => 'fasta');</div>
<div>$seqout->write_seq($seq);</div>
</div>
<div>======================================================</div>
<div>I use following command to run your script, both example files are in the working directory</div>
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<div>./<a href="http://parser.pl" target="_blank">parser.pl</a></div>
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<div>Out put is fasta sequence from "genomic-seq.fasta".</div>
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<div>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?</div>
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<div>Thanks a lot for your kind help.</div>
<div>Firoz</div>
<div>NYU, USA</div>
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</blockquote></div><br></div></div></div></div>