Add script to generate ortholog association files from GO Ath file

svn path=/; revision=668

diff --git a/interactome_scripts/association_file_from_orthologs.pl b/interactome_scripts/association_file_from_orthologs.pl
new file mode 100755 (executable)
index 0000000..66e327c
--- /dev/null
+++ b/interactome_scripts/association_file_from_orthologs.pl
@@ -0,0 +1,96 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+use Time::localtime;
+my $tm=localtime;
+my ($day,$month,$year)=($tm->mday,$tm->mon,$tm->year);
+my $curr_date = "$year$month$day";
+
+
+# check for arguments and explain usage
+if ($#ARGV !=3) {
+       print "usage: association_file_from_orthologs.pl in_assoc_file gene_name_file ortho_file out_file\n";
+       exit;
+}
+
+# Grab the find_species subroutines to get the species and taxon id
+if(-e "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl") {
+       require "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl";
+}elsif(-e "$ENV{HOME}/bin/find_species.pl") {
+       require "$ENV{HOME}/bin/find_species.pl";
+}
+
+
+my $ingaffile = $ARGV[0];
+my $ingenefile = $ARGV[1];
+my $inorthofile = $ARGV[2];
+my $outfile = $ARGV[3];
+
+# Get species and taxon
+my $species = find_species("$ingaffile");
+my $found_taxon = find_taxon($species);
+
+my %gene_hash;
+# hash to store symbol->gene lookups
+open (INGENEFILE, $ingenefile);
+while(<INGENEFILE>) {
+               my $line = $_;
+               chomp $line;
+               my ($gene, $description, $trembl, $swissprot, $uniprot) = split("\t", $line);
+               if($swissprot ne "") {
+                               $gene_hash{$swissprot}->{'gene'} = $gene;
+                               $gene_hash{$swissprot}->{'description'} = $description;
+               }
+               
+               if($uniprot ne "") {
+                               $gene_hash{$uniprot}->{'gene'} = $gene;
+                               $gene_hash{$uniprot}->{'description'} = $description;
+               }
+               
+}
+close(INGENEFILE);
+
+my %ortho_hash;
+open (INORTHOFILE, $inorthofile);
+while(<INORTHOFILE>) {
+               my $line = $_;
+               chomp $line;
+               next if ($line =~ /^id/);
+               my ($id, $gene, $ortho, $score) = split("\t", $line);
+               
+               if($score > "0.05") {
+                               $ortho_hash{$gene} = $ortho;
+               }
+}
+close(INORTHOFILE);
+               
+
+open (INGAFFILE, $ingaffile);
+open (OUTFILE, ">$outfile");
+
+print OUTFILE "!gaf-version: 2.0\n";
+print OUTFILE "!Created via ortholog similiarity from Arabidopsis thaliana\n";
+while(<INGAFFILE>) {
+               my $line = $_;
+               chomp $line;
+               #skip comments
+               next if ($line =~ /^!/);
+               
+               my ($db,$db_id,$db_symbol,$qual,$ont_id,$db_ref,$ev,$with,$aspect,$db_obj_name,$db_obj_syn,$db_obj_type,$taxon,$date,$assigned_by,$annot_ext,$gp_form_id) = split("\t", $line);
+               #skip with evidence codes IEA and ISS
+               next if ($ev eq "IEA");
+               next if ($ev eq "ISS");
+               #check if symbol found in %gene_hash
+               if(defined($gene_hash{$db_id})) {
+                               if(defined($ortho_hash{$gene_hash{$db_id}->{'gene'}})) {
+                                               my $ortho_gene = $ortho_hash{$gene_hash{$db_id}->{'gene'}};
+                                               my $ortho_desc = $gene_hash{$db_id}->{'description'};
+                                               print OUTFILE "$db\t$ortho_gene\t$ortho_gene\t$qual\t$ont_id\t$db_ref\t$ev\tUniProtKB:$gene_hash{$db_id}->{'gene'}\t$aspect\t$ortho_desc\t$db_obj_syn\t$db_obj_type\ttaxon:$found_taxon\t$curr_date\tJustin_Elser\t$annot_ext\t$gp_form_id\n";
+                               }
+               }
+               
+}
+close(INGAFFILE);
+close(OUTFILE);

diff --git a/interactome_scripts/association_file_from_orthologs_simple.pl b/interactome_scripts/association_file_from_orthologs_simple.pl
new file mode 100755 (executable)
index 0000000..16e7dca
--- /dev/null
+++ b/interactome_scripts/association_file_from_orthologs_simple.pl
@@ -0,0 +1,74 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+use Time::localtime;
+my $tm=localtime;
+my ($day,$month,$year)=($tm->mday,$tm->mon,$tm->year);
+$year += 1900;
+$month = sprintf '%02d', $month+1;
+$day = sprintf '%02d', $day;
+my $curr_date = "$year$month$day";
+print "$curr_date\n";
+
+
+
+# check for arguments and explain usage
+if ($#ARGV !=2) {
+       print "usage: association_file_from_orthologs.pl in_assoc_file ortho_file out_file\n";
+       exit;
+
+       
+# Grab the find_species subroutines to get the species and taxon id
+if(-e "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl") {
+       require "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl";
+}elsif(-e "$ENV{HOME}/bin/find_species.pl") {
+       require "$ENV{HOME}/bin/find_species.pl";
+}
+
+
+my $ingaffile = $ARGV[0];
+my $inorthofile = $ARGV[1];
+my $outfile = $ARGV[2];
+
+# Get species and taxon
+my $species = find_species("$ingaffile");
+my $new_taxon = find_taxon($species);
+
+
+my %ortho_hash;
+open (INORTHOFILE, $inorthofile);
+while(<INORTHOFILE>) {
+               my $line = $_;
+               chomp $line;
+               next if ($line =~ /^id/);
+               my ($gene, $ortho) = split("\t", $line);
+
+               $ortho_hash{$ortho} = $gene;
+
+}
+close(INORTHOFILE);
+               
+
+open (INGAFFILE, $ingaffile);
+open (OUTFILE, ">$outfile");
+
+print OUTFILE "!gaf-version: 2.0\n";
+print OUTFILE "!Created via ortholog similiarity from Arabidopsis thaliana\n";
+while(<INGAFFILE>) {
+               my $line = $_;
+               chomp $line;
+               #skip comments
+               next if ($line =~ /^!/);
+               
+               my ($db,$db_id,$db_symbol,$qual,$ont_id,$db_ref,$ev,$with,$aspect,$db_obj_name,$db_obj_syn,$db_obj_type,$taxon,$date,$assigned_by,$annot_ext,$gp_form_id) = split("\t", $line);
+               #check if symbol found in %gene_hash
+               if(defined($ortho_hash{$db_obj_name})) {
+                               my $ortho_gene = $ortho_hash{$db_obj_name};
+                               print OUTFILE "MaizeGDB\t$ortho_gene\t$ortho_gene\t$qual\t$ont_id\tPMID:24919147|PMID:21186353\tISO\tAGI_LocusCode:$db_obj_name\t$aspect\t$ortho_gene\t\t$db_obj_type\ttaxon:$new_taxon\t$curr_date\tPlanteome:Justin_Elser\t$annot_ext\t$gp_form_id\n";
+               }
+               
+}
+close(INGAFFILE);
+close(OUTFILE);