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Revision 1.1 - (download) (as text) (annotate)
Wed Feb 27 23:28:38 2008 UTC (11 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, 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
new

use FIGV;

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

my $complete = shift(@ARGV);

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

if($complete){
    my $input_file = "$jobdir/rp/$genome/Features/peg/fasta";
    `/vol/interpro-4.3/ppc/iprscan/bin/iprscan -cli -appl hmmpfam -iprlookup -goterms -i $input_file -o $jobdir/rp/$genome/iprscan_result_for_$genome.xml`;
}
else{
    my $fasta_file = "$jobdir/rp/$genome/partial_$genome.fa";
    open(INPUT_FILE,">$fasta_file");
    my %already;
    my @attributes = $fig->get_attributes(['fig|$genome.%'],'%_interpro_download');
    foreach my $attribute (@attributes){
	$already{@$attribute[0]} = 1;
    }

    my @pegs = $fig->pegs_of($genome);
    foreach my $peg (@pegs){
	if(! $already{$peg}){
	    my $seq = $fig->get_translation($peg);
	    print INPUT_FILE ">$peg\n$seq\n";
	}
    }
    close(INPUT_FILE);
    `/vol/interpro-4.3/ppc/iprscan/bin/iprscan -cli -appl hmmpfam -iprlookup -goterms -i $fasta_file -o $jobdir/rp/$genome/iprscan_result_for_$genome.xml`;
    
}

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