From 156b1451c71990a800bb3bdef567a7d05131cb20 Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Fri, 22 May 2015 21:32:36 +0000
Subject: [PATCH] Added script that parses NCBI taxonomy.dat file and creates
 slim OWL file, to be used by planteome.

svn path=/; revision=629
---
 .../planteome_ncbi_taxon_slimmer.pl           | 99 +++++++++++++++++++
 1 file changed, 99 insertions(+)
 create mode 100755 interactome_scripts/planteome_ncbi_taxon_slimmer.pl

diff --git a/interactome_scripts/planteome_ncbi_taxon_slimmer.pl b/interactome_scripts/planteome_ncbi_taxon_slimmer.pl
new file mode 100755
index 0000000..a74e3ee
--- /dev/null
+++ b/interactome_scripts/planteome_ncbi_taxon_slimmer.pl
@@ -0,0 +1,99 @@
+#!/usr/bin/perl
+
+###############################################################
+#  Justin Elser  (elserj@science.oregonstate.edu)             #
+#		Parses the assoc files for any taxon ids              #
+#		used in planteome assoc files.  Uses that to          #
+#		generate small (slim) subset of the ncbi taxonomy     #
+#		dat file.  From there, uses the owltools			  #
+#		ncbi2owl.jar program to generate OWL file             #
+#                                                             #
+###############################################################
+
+
+use strict;
+use warnings;
+
+# check for arguments and explain usage
+if ($#ARGV !=2) {
+	print "usage: planteome_ncbi_taxon_slimmer.pl taxonomy.dat_file taxonomy_slim_file output_OWL_file\n";
+	exit;
+}
+
+my $taxon_file = $ARGV[0];
+my $slim_file = $ARGV[1];
+my $output_file = $ARGV[2];
+
+my $ncbi_owltools_path = "/home/justin/owltools/OWLTools-NCBI/bin/ncbi2owl.jar";
+
+# open the assoc files to be parsed, assume this is all sqltable* files in directory
+
+my @files = glob("*.assoc");
+
+my %taxon_hash;
+# taxon id 1 is required, I think
+$taxon_hash{1} = 1;
+
+# get the relevant taxon ids
+foreach my $input_file (@files) {
+	open(INFILE, "$input_file") || die "Error: file '$input_file' can not be opened\n";
+	while(<INFILE>){
+			my $line = $_;
+			chomp $line;
+			
+			if($line =~ /taxon:(\d+)/) {
+					my $taxon = $1;
+					if(!defined($taxon_hash{$taxon})){
+							$taxon_hash{$taxon} = $taxon;
+					}
+			}
+	}
+	close(INFILE);
+}
+
+
+
+# Read in the full taxon file from ncbi and output only the entries that have matching taxon ids
+open(TAXONFILE, "$taxon_file") || die "Error: file '$taxon_file' can not be opened\n";
+open(TAXONSLIM, ">$slim_file") || die "Error: file '$slim_file' can not be opened for writing\n";
+my $keep_section = 0;
+while(<TAXONFILE>){
+		my $line = $_;
+		chomp $line;
+		
+		if($line =~ /^ID\s+:\s(\d+)/) {
+				if(defined($taxon_hash{$1})) {
+						print TAXONSLIM "$line\n";
+						$keep_section = 1;
+						next;
+				}
+		}
+		
+		if($keep_section == 1) {
+				print TAXONSLIM "$line\n";
+		}
+		
+		if($line =~ /^\/\//) {
+				$keep_section = 0;
+		}
+}
+				
+						
+system("java -Xmx6G -jar $ncbi_owltools_path $slim_file $output_file");
+						
+						
+						
+						
+						
+						
+						
+						
+						
+						
+						
+						
+						
+						
+						
+						
+						
-- 
2.34.1