From cf9f6d5efd49b02b9c4441f1bc693bc4e4f86cf0 Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Fri, 3 Sep 2010 00:02:12 +0000
Subject: [PATCH] Fix to skip all isomers, even if higher than .29

svn path=/; revision=22
---
 .../inparanoid_output_parse.pl                | 133 +++---------------
 1 file changed, 16 insertions(+), 117 deletions(-)

diff --git a/interactome_scripts/inparanoid_output_parse.pl b/interactome_scripts/inparanoid_output_parse.pl
index 8f64b9a..8c035b5 100755
--- a/interactome_scripts/inparanoid_output_parse.pl
+++ b/interactome_scripts/inparanoid_output_parse.pl
@@ -9,6 +9,8 @@
 #     Seems to work fine                                      #
 #  Version 1.01 - Nov 4 '09                                   #
 #     Added support for strawberry                            #
+#  Version 1.1 - April 2010                                   #
+#     Changed to use external subs to find species            #
 #                                                             #
 ###############################################################
 
@@ -19,6 +21,8 @@ use warnings;
 use DBI;
 use Term::Screen::ReadLine;
 
+require "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl";
+
 # open the file to be parsed, assume this is all sqltable* files in directory
 
 my @files = glob("sqltable*");
@@ -59,6 +63,8 @@ foreach my $input_file (@files) {
 	my $clust_table = "clusters";
 
 	my %id_hash;
+	
+	print "Working on $species_table\n";
 
 
 	
@@ -107,6 +113,16 @@ foreach my $input_file (@files) {
 		
 		# skip isomers that are not .1
 		next if ($gene =~ /\.[2-9]$/);
+		next if ($gene =~ /\.1[0-9]$/);
+		next if ($gene =~ /\.2[0-9]$/);
+		next if ($gene =~ /\.3[0-9]$/);
+		next if ($gene =~ /\.4[0-9]$/);
+		next if ($gene =~ /\.5[0-9]$/);
+		next if ($gene =~ /\.6[0-9]$/);
+		next if ($gene =~ /\.7[0-9]$/);
+		next if ($gene =~ /\.8[0-9]$/);
+		next if ($gene =~ /\.9[0-9]$/);
+		# assume there are never more than 29 isomers
 	
 		if(!defined($id_hash{$clust_id})) {
 			if ($clust_id ne $clust_id_prev) {
@@ -135,120 +151,3 @@ foreach my $input_file (@files) {
 $dbh->disconnect;
 	
 
-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/) {
-		$temp = "Soy";
-	}elsif ($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 =~ /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 = "Grape";
-	}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") {
-		$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") {
-		$gene = $gene_header;
-	}elsif ($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 "Soy") {
-		my ($name,$locus_id,$scaff_id,$isomer) = split(/\|/,$gene_header);
-		$gene = $isomer;
-	}elsif ($species eq "Human") {
-		$gene = $gene_header;
-	}elsif ($species eq "Maize") {
-		$gene = $gene_header;
-	}elsif ($species eq "Mouse") {
-		$gene = $gene_header;
-	}elsif ($species eq "Neurospora") {
-		$gene = $gene_header;
-	}elsif ($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 "Sacc_cerevisiae") {
-		$gene = $gene_header;
-	}elsif ($species eq "Sacc_pombe") {
-		$gene = $gene_header;
-	}elsif ($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 "Grape") {
-		my ($name,$gene_id,$chrom_id,$id) = split(/\|/,$gene_header);
-		$gene = $gene_id; #???
-	}else {
-		die "Error: Gene id can not be found!";
-	}
-	return $gene;
-}
-		
-		
-
-
-- 
2.34.1