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Annotation of /FortyEight/rp_submit_genome_to_iprscan_on_biocluster.pl

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1 : mkubal 1.1 use FIGV;
2 :    
3 :     my $jobdir = shift(@ARGV);
4 :     my $genome = shift(@ARGV);
5 :    
6 :     my $complete = shift(@ARGV);
7 :    
8 :     my $fig = new FIGV("$jobdir/rp/$genome");
9 :    
10 :     if($complete){
11 :     my $input_file = "$jobdir/rp/$genome/Features/peg/fasta";
12 :     `/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`;
13 :     }
14 :     else{
15 :     my $fasta_file = "$jobdir/rp/$genome/partial_$genome.fa";
16 :     open(INPUT_FILE,">$fasta_file");
17 :     my %already;
18 :     my @attributes = $fig->get_attributes(['fig|$genome.%'],'%_interpro_download');
19 :     foreach my $attribute (@attributes){
20 :     $already{@$attribute[0]} = 1;
21 :     }
22 :    
23 :     my @pegs = $fig->pegs_of($genome);
24 :     foreach my $peg (@pegs){
25 :     if(! $already{$peg}){
26 :     my $seq = $fig->get_translation($peg);
27 :     print INPUT_FILE ">$peg\n$seq\n";
28 :     }
29 :     }
30 :     close(INPUT_FILE);
31 :     `/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`;
32 :    
33 :     }

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