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Revision 1.2 - (download) (as text) (annotate)
Mon Apr 2 18:54:55 2007 UTC (12 years, 7 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

open(IN,"/vol/seed-attributes/computation_results/pdb_seqres_blast_output.txt");
open(OUT1,">/vol/seed-attributes/PDB/PDB_attributes.txt");

my $pdb;
my $peg;
my $score;
my %peg_to_pdb;
my %peg_to_score;
my $record;
my $record_start;
my %peg_to_start;
my %peg_to_stop;

while( $_ = <IN>){
    if($_ =~/Query=\s(\w+)_/){
	$pdb = $1;
        $record = 0;
    }
    if($_ =~/^(fig\|\d+.\d+.peg.\d+)\s+(\d+)\s+(\d+e-\d+)?/){
	$peg = $1;
	$score = $3;
	if($peg_to_pdb{$peg}){
	    $stored_score = $peg_to_score{$peg};
	    if($score < $stored_score){
		$peg_to_pdb{$peg} = $pdb;
		$peg_to_score{$peg} = $score;
	    }
	}
	else{
	    $peg_to_pdb{$peg} = $pdb;
	    $peg_to_score{$peg} = $score;
	}
	
    }
    
    if($_ =~/^>/){
       	if($_ =~/(fig\|.*)/){
	    $peg = $1;
	    if($peg_to_score{$peg}){$record = 1;$record_start =1;}
	    else{$record = 0}
	}
	else{$record = 0;}
    }
    
    if($record){
	if($record_start){
	    if($_ =~/Query:\s(\d+)/){
		$start = $1;
		$record_start = 0;
		$peg_to_start{$peg} = $start;
	    }
	}
	
	if($_ =~/Query:\s\d+.*\s(\d+)$/){
	    $stop = $1;
	    $peg_to_stop{$peg} = $stop;
	}
    }
}

foreach $peg (keys(%peg_to_pdb)){
    $pdb = $peg_to_pdb{$peg};
    $score = $peg_to_score{$peg};
    if($score =~/(\d+)e-(\d+)/){
	$part1 = $1;
	$part2 = $2;
	if($part2 > 19){
	    $part2 = (1000 - $part2);
	    $part1 = $part1 * 100;
	    $score = $part2.".".$part1;
            $start = $peg_to_start{$peg};
	    $stop = $peg_to_stop{$peg};
	    if($start){
		print OUT1 "$peg\tPDB::$pdb\t$score;$start-$stop\n";
	    }
	    else{
		print OUT1 "$peg\tPDB::$pdb\t$score\n";
	    }
	}
    }
}

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