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How To Parse a BLAST data file

by alyssa118 (Initiate)
on Apr 29, 2013 at 00:46 UTC ( #1031133=perlquestion: print w/ replies, xml ) Need Help??
alyssa118 has asked for the wisdom of the Perl Monks concerning the following question:

Hi Monks, I'm having a really hard time scanning an XML file from BLAST in perl. First, I need to search for a species name and then within that species, search for the highest hit score. Any tips?

Comment on How To Parse a BLAST data file
Re: How To Parse a BLAST data file
by ww (Bishop) 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.

    If you didn't program your executable by toggling in binary, it wasn't really programming!

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!
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....
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

      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

Re: How To Parse a BLAST data file
by bioinformatics (Friar) on Apr 29, 2013 at 15:59 UTC

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