Revision
1.3 -
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Wed Oct 17 15:32:50 2007 UTC
(12 years, 1 month 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, 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: +3 -3 lines
writes/reads to /rp/genome
my $jobdir = shift(@ARGV);
my $genome = shift(@ARGV);
my $date = localtime();
opendir(DIR,$jobdir."/rp/$genome");
if(! -d "$jobdir/rp/$genome/attributes"){
`mkdir $jobdir/rp/$genome/attributes`;
}
open(PHOB,">$jobdir/rp/$genome/attributes/PHOBIUS_attributes_for_$genome.txt");
my @files = readdir(DIR);
print PHOB "$genome\tPhobius_run_on_remote_server\t$date\n";
foreach my $file (@files){
if ($file =~/($genome.peg.\d+).PHOBIUS_result/){
my $peg = "fig|".$1;
open(IN,$jobdir."/rp/$genome/$file");
my @tm_locations = ();
while ($_ = <IN>){
if($_ =~/SIGNAL\s+(\d+)\s+(\d+)/){
print PHOB "$peg\tPhobius::signal\t$1-$2\n";
}
if($_ =~/TRANSMEM\s+(\d+)\s+(\d+)/){
my $loc = "$1-$2";
push(@tm_locations,$loc);
}
}
close(IN);
if(scalar(@tm_locations) > 0){
my $loc_string = join(",",@tm_locations);
print PHOB "$peg\tPhobius::transmembrane\t$loc_string\n";
}
}
}
close(PHOB);
`rm $jobdir/rp/$genome/*.PHOBIUS_result`;
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