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Revision 1.1 - (download) (as text) (annotate)
Wed Feb 18 22:09:47 2009 UTC (10 years, 8 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, mgrast_dev_05262011, mgrast_dev_04082011, rast_rel_2010_0928, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, rast_rel_2011_0119, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, mgrast_dev_04012011, rast_rel_2009_07_09, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, HEAD
Convert full blast output to -m8 output using  Gary's blast parsing code.

use gjoparseblast;
use strict;
use Data::Dumper;
use FileHandle;

my $input;
if (@ARGV == 0)
{
    $input = \*STDIN;
}
else
{
    my $f = shift;
    $input = new FileHandle("<$f");
    $input or die "Cannot open $f: $!";
}

my $n;

#
# 6: scr = bit-score
# 7: e_val
# 8 p_n k

while (my $record = next_blast_hsp($input, 0))
{
    my($qid, $qdef, $qlen, $sid, $sdef, $slen, $scr, $e_val, $p_n, $p_val, $n_mat, $n_id, $n_pos, $n_gap, $dir, $q1, $q2, $qseq, $s1, $s2, $sseq) = @$record;
#    $record->[17] = $record->[20] = '';
#    print Dumper($record);

    print join("\t", $qid, $sid, sprintf("%.2f", 100 * $n_id / $n_mat), $n_mat, $n_mat - $n_id - $n_gap, $n_gap, $q1, $q2, $s1, $s2, $e_val, $scr, $qlen, $slen), "\n";
}


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