How To Parse a BLAST data file

alyssa118 has asked for the wisdom of the Perl Monks concerning the following question:

Replies are listed 'Best First'.
Re: How To Parse a BLAST data file by ww (Archbishop) on Apr 29, 2013 at 02:26 UTC
Yeah. Several. None of them, however, amount to code-a-matic output. We try not to do that here. Show some effort: On asking for help and How do I post a question effectively? Check out a bioperl site or do your due diligence here, by searching (Super Search) for similar problems Update your node when you've done some work: show it to us and tell us how it fails if it's not doing the job you're attempting as you expected If you didn't program your executable by toggling in binary, it wasn't really programming!	[reply]
Re: How To Parse a BLAST data file by bioinformatics (Friar) on Apr 29, 2013 at 15:59 UTC
This is where I would recommend using bioperl. You can find the modules here: http://bioperl.org/wiki/Main_Page. Specific examples for parsing blast searches are here: http://bioperl.org/wiki/HOWTO:SearchIO#Using_SearchIO. If you don't have administrative permissions on the machine you are using, you can clone the git repository and export the location to $PERL5LIB. Bioinformatics	[reply]
Re: How To Parse a BLAST data file by Rahul6990 (Beadle) on Apr 29, 2013 at 05:37 UTC
Refer to this tutorial. Happy Programming....	[reply]
Re^2: How To Parse a BLAST data file by Anonymous Monk on Apr 29, 2013 at 06:56 UTC
Refer to this tutorial. Um, no, XML::Parser is very low level. The standard way to parse XML is DOM + XPATH, say using XML::Twig, XML::LibXML, Mojo::DOM ... see Re: The best module for handling xml for examples, walkthroughs, follow my links and the links they link, like these Re: How to grab a portion of file with regex (don't)(parsing html/xml with xpath/twig/dom, because html::parser is low level), Re: How to grab a portion of file with regex (parsing html/xml with xpath/twig/dom, because xml::parser is low level), Re^4: How to grab a portion of file with regex (parsing html/xml with xpath/twig/dom, because ::parser is low level)	[reply]
Re: How To Parse a BLAST data file by perll12 (Initiate) on Apr 29, 2013 at 03:35 UTC
it's okay! keep trying! you'll get there!	[reply]
Re: How To Parse a BLAST data file by Anonymous Monk on Apr 29, 2013 at 08:27 UTC
Hi alyssa118, Could you post the xml file onto your scratchpad? I'm quite familiar with BLAST so I'll try to help. Cathy	[reply]
Re^2: How To Parse a BLAST data file by talexb (Chancellor) on Apr 29, 2013 at 15:18 UTC
No, don't ask someone to post it on their scratchpad. The point of including the XML in the post is so that someone can look at this in a year's time (or ten year's time) and get something out of it. The scratchpad's contents may be gone next week, leaving a big hole in the story behind this problem. Alex / talexb / Toronto "Groklaw is the open-source mentality applied to legal research" ~ Linus Torvalds	[reply]