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Revision 1.3 - (download) (as text) (annotate)
Mon Apr 2 18:54:19 2007 UTC (12 years, 8 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 1.2: +1 -2 lines
fix to score format

$genome = shift(@ARGV);
open(IN,"/vol/seed-attributes/computation_results/iprscan_results_for_$genome");
open(IPR,">/vol/seed-attributes/IPR/IPR_attributes_for_$genome.txt");
open(PFAM,">/vol/seed-attributes/PFAM/PFAM_attributes_for_$genome.txt");
open(GO,">/vol/seed-attributes/GO/GO_attributes_for_$genome.txt");

my $id;
my $goid;
my $description;
my $pf;
my $ipr;
my $record_ipr;
    
while ($_ = <IN>){
    if($_ =~/(\d+.\d.peg.\d+)/){
	$id = $1;
	$id = "fig|".$id;
	$record_ipr = 1;
    }
    
    if($record_ipr){
	if($_ =~/interpro id=\"(IPR\d+)\"/){
	    $ipr = $1;
	    $record_ipr = 0;
	}
    }
    
    if($_ =~/GO:(\d+)/){
	$goid = $1;
    }
    
    if($_ =~/<description>(.*)<\/description/){
	$description = $1;
	print GO "$id\tGO\t$goid\n";
    }
    
    if($_ =~/(PF\d+)/){
	$pf = $1;
    }
    
    if($_ =~/location start=\"(\d+)\"\send=\"(\d+)\"\sscore=\"(.*)\"\sstatus/){
	$start = $1;
	$end = $2;
	$score = $3;
	if($score =~/(\d+)e-(\d+)/){
	    $part1 = $1;
	    $part2 = $2;
	    if($part2 > 19){
		$part2 = (1000 - $part2);
		$part1 = $part1 * 100;
		$score = $part2.".".$part1;
		print PFAM "$id\tPFAM::$pf\t$score;$start-$end\n";
		print IPR "$id\tIPR::$ipr\t$score;$start-$end\n";
	    }
	}
	if($score eq "0"){
	    print PFAM "$id\tPFAM::$pf\t0.0;$start-$end\n";
	    print IPR "$id\tIPR::$ipr\t0.0;$start-$end\n";
	}
    }
}
close(IN);


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