Fix to skip all isomers, even if higher than .29

svn path=/; revision=22

diff --git a/interactome_scripts/inparanoid_output_parse.pl b/interactome_scripts/inparanoid_output_parse.pl
index 8f64b9ab6bcd1f635a96b9f242b1fd14781bb4db..8c035b52295aee3561be3f0ba45ccda0aa98019f 100755 (executable)
--- 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;
-}
-               
-               
-
-