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get full hit descrption from blast output (xml)

by ejbiers (Initiate)
on Nov 29, 2012 at 21:58 UTC ( #1006367=perlquestion: print w/replies, xml ) Need Help??

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  1. or download this
    <?xml version="1.0"?>
    <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://ww
    +w.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
    <BlastOutput>
    ...
                </Hsp>
              </Hit_hsps>
            </Hit>
    
  2. or download this
    #!/usr/local/bin/perl
    
    # Usage information
    ...
    }
    main();
    print " DONE!!!\n";
    
  3. or download this
    query_name    query_length    accession_number    subject_length    su
    +bject_description    E value    bit score    frame    query_start    
    +query_end    hit_start    hit_end    %_conserved    %_identical
    HKUN3Y301D9XQX length=508 xy=1636_1159 region=1 run=R_2012_03_16_06_53
    +_48_    508    1515029    65    (Cyanothece ATCC 51142)    0.00664016
    +    40.0466    0    155    253    12    44    81.8%    51.5%
    

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Node Type: perlquestion [id://1006367]
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[ambrus]: Corion: some of these stupid syntax highlighters assume that too. just look at the table in http://perldoc. perl.org/ functions/pack. html for example.
[haukex]: ..."yet" ;-) I haven't had to deal with Dist::Zilla yet but I've heard about how it's a big setup
[ambrus]: I really don't like automagic stuff. I'm happy when computers do exactly what I tell them, even if that means they sometimes do the wrong thing.
[ambrus]: And I don't much like syntax highlighters. If you need a syntax highlighter to understand your code, then your code is written unclear.
[ambrus]: And if you need a syntax highlighter to color parenthesis green and numbers black and letters blue, then you're using the wrong font.
[ambrus]: I have to tolerate syntax highlighters when other people use them, but I don't use them myself. And sorry for the rant.

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