From: elserj <elserj@localhost>
Date: Mon, 5 Apr 2010 20:09:48 +0000 (+0000)
Subject: added the script that has the find_species and find_gene subroutines
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=ae813a85d4026d43f1d05e871fb307013c3e05ba;p=old-jaiswallab-svn%2F.git

added the script that has the find_species and find_gene subroutines

svn path=/; revision=13
---

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
new file mode 100755
index 0000000..17c7a88
--- /dev/null
+++ b/interactome_scripts/find_species.pl
@@ -0,0 +1,136 @@
+###########################################################
+#  Common subroutines to find the species from the        #
+#    string (filename) and the gene from the gene header  #
+#                                                         #
+###########################################################
+
+sub find_species {
+	my $temp = $_[0];
+	if ($temp =~ /Arabidopsis/) {
+		$temp = "Ath";
+	}elsif ($temp =~ /brachypodium/) {
+		$temp = "Brachy";
+	}elsif ($temp =~ /elegans/) {
+		$temp = "C_elegans";
+	}elsif ($temp =~ /Chlamy/) {
+		$temp = "Chlamy";
+	}elsif ($temp =~ /Danio/) {
+		$temp = "Danio";
+	}elsif ($temp =~ /E\_coli/) {
+		$temp = "E_coli";
+	}elsif ($temp =~ /Fragaria/) {
+		$temp = "Fragaria";
+	}elsif ($temp =~ /Glycine/) {
+		$temp = "Glycine";
+	}elsif ($temp =~ /Homo\_sapiens/) {
+		$temp = "Human";
+	}elsif ($temp =~ /Maize/) {
+		$temp = "Maize";
+	}elsif ($temp =~ /musculus/) {
+		$temp = "Mouse";
+	}elsif ($temp =~ /neurospora/) {
+		$temp = "Neurospora";
+	}elsif ($temp =~ /Oryza\_sativa/) {
+		$temp = "Oryza_sativa";
+	}elsif ($temp =~ /Physcomit/) {
+		$temp = "Physcomitreall";
+	}elsif ($temp =~ /Populus/) {
+		$temp = "Poplar";
+	}elsif ($temp =~ /Ppersica/) {
+		$temp = "P_persica";
+	}elsif ($temp =~ /cerevisiae/) {
+		$temp = "Sacc_cerevisiae";
+	}elsif ($temp =~ /pombe/) {
+		$temp = "Sacc_pombe";
+	}elsif ($temp =~ /Selaginella/) {
+		$temp = "Selaginella";
+	}elsif ($temp =~ /Sorghum/) {
+		$temp = "Sorghum";
+	}elsif ($temp =~ /Synechosystis/) {
+		$temp = "Synechosystis";
+	}elsif ($temp =~ /Vitis\_vinifera/) {
+		$temp = "Vitis";
+	}else {
+		die "Error: Species can not be found from file name!";
+	}
+	return $temp;
+}
+
+sub find_gene {
+	my $gene_header = $_[0];
+	my $species = $_[1];
+	my $gene;
+	if ($species eq "Ath") {
+		my ($name,$gene_id,$chrom,$isomer) = split(/\|/, $gene_header);
+		$gene = $isomer;
+	}elsif ($species eq "Brachy") {
+		#uncomment for newer version of fasta file
+		#my ($gene_id,$chrom,$isomer,$name) = split(/\|/, $gene_header);
+		#$gene = $isomer;
+		#uncomment for old version of fasta file
+		$gene = $gene_header;
+	}elsif ($species eq "C_elegans") {
+		my ($gene_id,$temp) = split(/\|/, $gene_header);
+		$gene = $gene_id; #???
+	}elsif ($species eq "Chlamy") {
+		my ($name,$locus_id,$scaff_id,$temp) = split(/\|/,$gene_header);
+		$gene = $locus_id; #???
+	}elsif ($species eq "Danio") {
+		my ($gene_id,$temp) = split(/\s/,$gene_header);
+		$gene = $gene_id;
+	}elsif ($species eq "E_coli") {
+		$gene = $gene_header; #???
+	}elsif ($species eq "Fragaria") {
+		my ($gene_id, $mrna_id, $method, $length) = split(/\|/, $gene_header);
+		$gene = $gene_id;
+	}elsif ($species eq "Glycine") {
+		my ($name,$locus_id,$scaff_id,$isomer) = split(/\|/,$gene_header);
+		$gene = $isomer;
+	}elsif ($species eq "Human") {
+		my ($gene_id,$temp) = split(/\s/,$gene_header);
+		$gene = $gene_id;
+	}elsif ($species eq "Maize") {
+		$gene = $gene_header;
+	}elsif ($species eq "Mouse") {
+		my ($gene_id,$temp) = split(/\s/,$gene_header);
+		$gene = $gene_id;
+	}elsif ($species eq "Neurospora") {
+		my ($gene_id,$temp) = split(/\s/,$gene_header);
+		$gene = $gene_id;
+	}elsif ($species eq "Oryza_sativa") {
+		my ($isomer,$temp,$type) = split(/\|/,$gene_header);
+		$gene = $isomer;
+	}elsif ($species eq "Physcomitreall") {
+		my ($name,$locus_id,$chrom_id,$prot_id) = split(/\|/,$gene_header);
+		$gene = $prot_id; #???
+	}elsif ($species eq "Poplar") {
+		my ($name,$locus_id,$chrom_id,$prot_id) = split(/\|/,$gene_header);
+		$gene = $prot_id; #???
+	}elsif ($species eq "P_persica") {
+		my ($gene_id,$temp) = split(/\s/,$gene_header);
+		$gene = $gene_id;
+	}elsif ($species eq "Sacc_cerevisiae") {
+		my ($gene_id,$temp) = split(/\s/,$gene_header);
+		$gene = $gene_id;
+	}elsif ($species eq "Sacc_pombe") {
+		my ($gene_id,$temp) = split(/\s/,$gene_header);
+		$gene = $gene_id;
+	}elsif ($species eq "Selaginella") {
+		my ($name,$locus_id,$chrom_id,$prot_id) = split(/\|/,$gene_header);
+		$gene = $prot_id; #???
+	}elsif ($species eq "Sorghum") {
+		my ($name,$locus_id,$scaff_id,$prot_id) = split(/\|/,$gene_header);
+		$gene = $prot_id; #???
+	}elsif ($species eq "Synechosystis") {
+		my ($gene_id,$type,$temp) = split(" ",$gene_header);
+		$gene = $gene_id; #???
+	}elsif ($species eq "Vitis") {
+		my ($name,$gene_id,$chrom_id,$id) = split(/\|/,$gene_header);
+		$gene = $gene_id; #???
+	}else {
+		die "Error: Gene id can not be found!";
+	}
+	return $gene;
+}
+
+1;