<div dir="ltr"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;color:rgb(0,0,0)">Hello again,</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;color:rgb(0,0,0)"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;color:rgb(0,0,0)">Please find below the code I used to parse a regular BLASTX report. I confirm that the problem also happens with frac_aligned_hit().</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;color:rgb(0,0,0)"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;color:rgb(0,0,0)">Any help is appreciated.</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;color:rgb(0,0,0)">Best,</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;color:rgb(0,0,0)">Thiago</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;color:rgb(0,0,0)"><br></div><div class="gmail_default"><div class="gmail_default"><font face="times new roman, serif" color="#0000ff">use strict;</font></div><div class="gmail_default"><font face="times new roman, serif" color="#0000ff">use warnings;</font></div><div class="gmail_default"><font face="times new roman, serif" color="#0000ff">use Bio::SearchIO;</font></div><div class="gmail_default"><font face="times new roman, serif" color="#0000ff"><br></font></div><div class="gmail_default"><font face="times new roman, serif" color="#0000ff">my $searchio = Bio::SearchIO->new( -format => 'blast',</font></div><div class="gmail_default"><font face="times new roman, serif" color="#0000ff"><span style="white-space:pre-wrap"> </span> -file => shift );</font></div><div class="gmail_default"><font face="times new roman, serif" color="#0000ff"><br></font></div><div class="gmail_default"><font face="times new roman, serif" color="#0000ff">while ( my $result = $searchio->next_result() ) {</font></div><div class="gmail_default"><font face="times new roman, serif" color="#0000ff"><br></font></div><div class="gmail_default"><font face="times new roman, serif" color="#0000ff"> while( my $hit = $result->next_hit ) {</font></div><div class="gmail_default"><span style="white-space:pre-wrap"><font face="times new roman, serif" color="#0000ff"> </font></span></div><div class="gmail_default"><font face="times new roman, serif" color="#0000ff"><span style="white-space:pre-wrap"> </span>print $hit->name."\t".$hit->frac_aligned_query."\n";</font></div><div class="gmail_default"><font face="times new roman, serif" color="#0000ff"> }</font></div><div class="gmail_default"><font face="times new roman, serif" color="#0000ff">}</font></div><div style="color:rgb(0,0,0);font-family:arial,helvetica,sans-serif"><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Dec 17, 2014 at 7:55 PM, Thiago M. Venancio <span dir="ltr"><<a href="mailto:thiago.venancio@gmail.com" target="_blank">thiago.venancio@gmail.com</a>></span> wrote:<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Chris,<div>Thanks.<span></span><br><div>I do not have the exact code rigth now, but it is very simple. The problem happens when I call the frac_aligned_query() on the hit object in Bio::SearchIO. I do not know a better way to get the coverage values. </div><div>Best,</div><div>Thiago<div><div class="h5"><br><br>On Wednesday, December 17, 2014, Fields, Christopher J <<a href="mailto:cjfields@illinois.edu" target="_blank">cjfields@illinois.edu</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Thiago,
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<div>Best thing would be to see your code to try to understand what you are trying to do. It seems to be triggering the older HSP tiling code for BioPerl, and there may be better ways to get at the data (e.g. Mark Jensen’s work on refactoring HSP tiling into
a separate code base: <a href="http://www.bioperl.org/wiki/HOWTO:Tiling" target="_blank">http://www.bioperl.org/wiki/HOWTO:Tiling</a>).</div>
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<div>chris</div>
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<div>On Dec 17, 2014, at 12:04 PM, Thiago M. Venancio <<a>thiago.venancio@gmail.com</a>> wrote:</div>
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Hi all,</div>
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I am parsing a BLASTX report and got the following error for some sequences.</div>
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It always happen with sub-sequences of 1 base. I found some posts on this issue, but they are old.</div>
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I am use the latest version installed through cpan.</div>
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<b>$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'</b></div>
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<b>1.006924</b></div>
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Any help is appreciated.</div>
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Thiago</div>
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<br>
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------------- EXCEPTION: Bio::Root::Exception -------------</div>
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MSG: Undefined sub-sequence (241,242). Valid range = 96 - 242</div>
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STACK: Error::throw</div>
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STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472</div>
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STACK: Bio::Search::HSP::HSPI::matches /usr/share/perl5/Bio/Search/HSP/HSPI.pm:716</div>
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STACK: Bio::Search::SearchUtils::_adjust_contigs /usr/share/perl5/Bio/Search/SearchUtils.pm:431</div>
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STACK: Bio::Search::SearchUtils::tile_hsps /usr/share/perl5/Bio/Search/SearchUtils.pm:201</div>
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STACK: Bio::Search::Hit::GenericHit::frac_aligned_hit /usr/share/perl5/Bio/Search/Hit/GenericHit.pm:1319</div>
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-- <br>
<div>=================================<br>
Thiago Motta Venancio, M.Sc., PhD<br>
<a href="http://venancio.openwetware.org/" target="_blank">http://venancio.openwetware.org/</a><br>
=================================</div>
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</blockquote></div></div></div></div><div class="HOEnZb"><div class="h5"><br><br>-- <br>=================================<br>Thiago Motta Venancio, M.Sc., PhD<br><a href="http://venancio.openwetware.org/" target="_blank">http://venancio.openwetware.org/</a><br>=================================<br>
</div></div></blockquote></div><br clear="all"><div><br></div>-- <br><div class="gmail_signature">=================================<br>Thiago Motta Venancio, M.Sc., PhD<br><a href="http://venancio.openwetware.org/" target="_blank">http://venancio.openwetware.org/</a><br>=================================</div>
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