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Revision 1.2 - (download) (as text) (annotate)
Mon Apr 2 18:55:12 2007 UTC (13 years, 3 months ago) by mkubal
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, 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, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, 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, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.1: +1 -2 lines
fix to score format

$genome = shift(@ARGV);
open(IN,"/vol/seed-attributes/computation_results/CDD/$genome/rpsblast_results.txt");
open(OUT,">/vol/seed-attributes/CDD/CDD_attributes_for_$genome.txt");

my $peg, $id, $score, %id_score, %id_start,%id_stop,$record, $record_start,$start,$stop;
while ($_ = <IN>){
    chomp($_);
    if($_ =~/Query=\s(fig\|\d+.\d+.peg.\d+)/){
	$new_peg = $1;
	if($peg){
	    foreach $key (keys(%id_score)){
		$string = "$peg\tCDD::$key\t$id_score{$key};$id_start{$key}-$id_stop{$key}\n";
		if($string =~/(\d+-\d+)$/){print OUT "$string"}
	    }
	}
	$peg = $new_peg;
	foreach $key (keys(%id_score)){delete($id_score{$key})}
	foreach $key (keys(%id_start)){delete($id_start{$key})}
	foreach $key (keys(%id_stop)){delete($id_stop{$key})}
	$record = 0;
    }
    
    #handle last peg in file
    if($_ =~/\Database:\sCDD/){
	if($peg){
	    foreach $key (keys(%id_score)){
		print OUT "$peg\tCDD::$key\t$id_score{$key};$id_start{$key}-$id_stop{$key}\n";
	    }
	}
    }
    
    if($_ =~/\|CDD\|(\d+).*\s+(\d+e-\d+)$/){
	$id = $1;
	$score = $2;
	if($score =~/(\d+)e-(\d+)/){
	    $part1 = $1;
	    $part2 = $2;
	    if($part2 > 19){
		$part2 = (1000 - $part2);
		$part1 = $part1 * 100;
		$score = $part2.".".$part1;
		$id_score{$id} = $score;
	    }
	}
    }
    
    if($_ =~/>gnl\|CDD\|(\d+)\s/){
	$id = $1;
	if($id_score{$id}){$record = 1;$record_start =1;}
	else{$record = 0}
    }
	    
    if($record){
	if($record_start){
	    if($_ =~/Query:\s(\d+)/){
		$start = $1;
		$record_start = 0;
		$record_stop = 1;
		$id_start{$id} = $start;
	    }
	}
	if($_ =~/Query:\s\d+.*\s(\d+)$/){
	    $stop = $1;
	    $id_stop{$id} = $stop;
	}
    }
}



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