<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>Forgot to reply all, see below. Issue Resolved!<br><br>Travis Wrightsman</div><div><br>Begin forwarded message:<br><br></div><blockquote type="cite"><div><b>From:</b> Travis Wrightsman <<a href="mailto:twrig002@ucr.edu">twrig002@ucr.edu</a>><br><b>Date:</b> July 29, 2015 at 12:32:08 PM PDT<br><b>To:</b> Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>><br><b>Subject:</b> <b>Re: [Biopython-dev] Blast XML Parse Improvements</b><br><br></div></blockquote><blockquote type="cite"><div><span>That is an unfortunately labeled feature, hopefully NCBI will implement a subject-like feature that works the way we expect it to.</span><br><span></span><br><span>Thank you for the clarification!</span><br><span></span><br><span>Travis Wrightsman</span><br><span></span><br><blockquote type="cite"><span>On Jul 29, 2015, at 11:26 AM, Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>> wrote:</span><br></blockquote><blockquote type="cite"><span></span><br></blockquote><blockquote type="cite"><span>Hi Travis,</span><br></blockquote><blockquote type="cite"><span></span><br></blockquote><blockquote type="cite"><span>This is an NCBI "feature", not a Biopython bug.</span><br></blockquote><blockquote type="cite"><span></span><br></blockquote><blockquote type="cite"><span>Using -subject means BLAST does lots of pairwise comparisons,</span><br></blockquote><blockquote type="cite"><span>so you get lots of iteration blocks in the XML. To get the results</span><br></blockquote><blockquote type="cite"><span>you probably want (and meaningful e-values), first make a BLAST</span><br></blockquote><blockquote type="cite"><span>database. See:</span><br></blockquote><blockquote type="cite"><span></span><br></blockquote><blockquote type="cite"><span><a href="http://blastedbio.blogspot.co.uk/2012/05/blast-ingoring-search-space-size-for-e.html">http://blastedbio.blogspot.co.uk/2012/05/blast-ingoring-search-space-size-for-e.html</a></span><br></blockquote><blockquote type="cite"><span></span><br></blockquote><blockquote type="cite"><span>Regards,</span><br></blockquote><blockquote type="cite"><span></span><br></blockquote><blockquote type="cite"><span>Peter</span><br></blockquote><blockquote type="cite"><span></span><br></blockquote><blockquote type="cite"><blockquote type="cite"><span>On Wed, Jul 29, 2015 at 5:19 PM, Travis Wrightsman <<a href="mailto:twrig002@ucr.edu">twrig002@ucr.edu</a>> wrote:</span><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><span>Peter and others,</span><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><span>Here is the gist: <a href="https://gist.github.com/twrightsman/a94c66016692fd4295be">https://gist.github.com/twrightsman/a94c66016692fd4295be</a></span><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><span>The xml output shows the tool version and I included my shell commands used</span><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><span>to get the results; it is still using the "current" BLAST XML format with</span><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><span>iteration blocks.</span><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><span>-Travis</span><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><span>On Wed, Jul 29, 2015 at 1:44 AM, Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>></span><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><span>wrote:</span><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>Right, the new "blastxml2" output in BLAST+ 2.2.31 is a whole new format,</span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>but the existing "blastxml" which Biopython already has a parser for is</span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>still available as usual via -outfmt 5.</span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>And that parser ought to work fine with multiple queries.</span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>Travis, can you post more details? e.g. BLAST+ command line used</span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>and ideally sample output (on <a href="http://gist.github.com">gist.github.com</a> or similar)</span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>Thanks,</span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>Peter</span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>On Wed, Jul 29, 2015 at 6:29 AM, Fields, Christopher J</span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span><<a href="mailto:cjfields@illinois.edu">cjfields@illinois.edu</a>> wrote:</span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>Keep in mind there are significant changes for BLAST+ XML output in the</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>latest release, not all of them good IMHO. Peter has a pretty good</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>writeup</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>on this:</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span><a href="http://blastedbio.blogspot.com/2015/07/blast-xml-2-include-trouble.html">http://blastedbio.blogspot.com/2015/07/blast-xml-2-include-trouble.html</a></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>chris</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>On Jul 29, 2015, at 12:21 AM, Wibowo Arindrarto <<a href="mailto:w.arindrarto@gmail.com">w.arindrarto@gmail.com</a>></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>wrote:</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>Hi Travis,</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>There hasn't been any new test cases added for BLAST 2.2.30, as I</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>recall. Did you get the same behavior when using Bio.SearchIO to parse</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>it?</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>Best regards,</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>Bow</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>On Wed, Jul 29, 2015 at 7:12 AM, Travis Wrightsman <<a href="mailto:twrig002@ucr.edu">twrig002@ucr.edu</a>></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>wrote:</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>Biopython Devs,</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>I was trying to parse through a tblastn XML output with multiple queries</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>in</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>the query file and it was generating a BLAST record object for each</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>contig</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>in the subject file instead of each run. Is this the intended behavior</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>or</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>has this not been updated for ncbi tools 2.2.30?</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>If it needs to be updated or finished, I'm more than happy to rewrite or</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>update some of the code in NCBIXML for the latest version.</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>-Travis</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>_______________________________________________</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>Biopython-dev mailing list</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span><a href="mailto:Biopython-dev@mailman.open-bio.org">Biopython-dev@mailman.open-bio.org</a></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span><a href="http://mailman.open-bio.org/mailman/listinfo/biopython-dev">http://mailman.open-bio.org/mailman/listinfo/biopython-dev</a></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>_______________________________________________</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>Biopython-dev mailing list</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span><a href="mailto:Biopython-dev@mailman.open-bio.org">Biopython-dev@mailman.open-bio.org</a></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span><a href="http://mailman.open-bio.org/mailman/listinfo/biopython-dev">http://mailman.open-bio.org/mailman/listinfo/biopython-dev</a></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>_______________________________________________</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>Biopython-dev mailing list</span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span><a href="mailto:Biopython-dev@mailman.open-bio.org">Biopython-dev@mailman.open-bio.org</a></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span><a href="http://mailman.open-bio.org/mailman/listinfo/biopython-dev">http://mailman.open-bio.org/mailman/listinfo/biopython-dev</a></span><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>_______________________________________________</span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span>Biopython-dev mailing list</span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span><a href="mailto:Biopython-dev@mailman.open-bio.org">Biopython-dev@mailman.open-bio.org</a></span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><span><a href="http://mailman.open-bio.org/mailman/listinfo/biopython-dev">http://mailman.open-bio.org/mailman/listinfo/biopython-dev</a></span><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><span></span><br></blockquote></blockquote></div></blockquote></body></html>