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Revision 1.2 - (download) (as text) (annotate)
Mon May 5 14:12:58 2008 UTC (11 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, 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, 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: +2 -5 lines
v2

use Data::Dumper;
use Carp;
use FIG_Config;
use FIGV;

my $jobdir = shift(@ARGV);
my $genome = shift(@ARGV);
my $date = localtime();

if(! -d "$jobdir/rp/$genome/attributes"){
    `mkdir $jobdir/rp/$genome/attributes`;
}

my $fig = new FIGV("$jobdir/rp/$genome");

my $prefix;
if ($genome =~/(\d+)\.\d+/){
    $prefix = $1;
}

open(IN,"/vol/seed-attributes/Genome_Phenotype_Data/reformatted_phenotype_data_from_Liz_030308.txt");
while($_ = <IN>){
    chomp($_);
    my $ncbi;
    if($_ =~/^\d+\t(\d+)/){$ncbi = $1;}
    if($prefix eq $ncbi){
	@cols = split("\t",$_);
	my $output_dir = "$jobdir/rp/$genome/attributes";
	if(! -d $output_dir){
	    `mkdir $output_dir`;
	}
	
	open(OUT,">$output_dir/phenotypes.txt");
	print OUT "$genome\tGC_Content\t$cols[7]\n";
	if($cols[8] =~/-/){
	    print OUT "$genome\tGram_Stain\tNegative\n";
	}
	elsif($cols[8] =~/\+/){
	    print OUT "$genome\tGram_Stain\tPositive\n";
	}
	else{
	    print OUT "$genome\tGram_Stain\t$cols[8]\n";
	}
	print OUT "$genome\tShape\t$cols[9]\n";
	print OUT "$genome\tArrangement\t$cols[10]\n";
	print OUT "$genome\tEndospores\t$cols[11]\n";
	print OUT "$genome\tMotility\t$cols[12]\n";
	print OUT "$genome\tSalinity\t$cols[13]\n";
	print OUT "$genome\tOxygen_Requirement\t$cols[14]\n";
	print OUT "$genome\tHabitat\t$cols[15]\n";
	print OUT "$genome\tTemperature_Range\t$cols[16]\n";
	print OUT "$genome\tOptimal_Temperature\t$cols[17]\n";
	print OUT "$genome\tPathogenic\t$cols[18]\n";
	print OUT "$genome\tPathogenic_In\t$cols[19]\n";
	if($cols[20] =~/(.*\w)/){
	    print OUT "$genome\tDisease\t$1\n";
	}
	close(OUT);
	last;
    }
}



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