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<br><br>On Wednesday, December 17, 2014, Fields, Christopher J <<a href="mailto:cjfields@illinois.edu">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 href="javascript:_e(%7B%7D,'cvml','thiago.venancio@gmail.com');" target="_blank">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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------------- 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><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>