From: preecej <preecej@localhost>
Date: Thu, 7 Jun 2012 22:05:21 +0000 (+0000)
Subject: sew together SSR data from 3 different sample transcriptome assemblies
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=dcf554d919c6fe02fa832dd01f7e2d2513c10c82;p=old-jaiswallab-svn%2F.git

sew together SSR data from 3 different sample transcriptome assemblies
, correlate via BLAST, output SSR count differentials amongst resulting orthologs >
dimer

svn path=/; revision=345
---

diff --git a/Personnel/preecej/perl_singletons/brasy_ssr_mash.pl b/Personnel/preecej/perl_singletons/brasy_ssr_mash.pl
new file mode 100644
index 0000000..88cd1a7
--- /dev/null
+++ b/Personnel/preecej/perl_singletons/brasy_ssr_mash.pl
@@ -0,0 +1,143 @@
+#!/usr/bin/perl -w
+use strict;
+
+use Switch;
+use Data::Dumper;
+
+#perl script for ssr data
+
+$Data::Dumper::Pad = "... "; 
+
+#file handles
+my $esp_ssr = "./brasy-esp.ssr";
+my $gre_ssr = "./brasy-gre.ssr";
+my $cor_ssr = "./brasy-cor.ssr";;
+my $ortho = "./sylvaticum_orthologs.txt";
+
+# hashes
+my %esp;
+my %gre;
+my %cor;
+
+#load ssr data into hash keyed by spain gene id   
+#add ssr_words hash to the spain_id_gene_key
+#add first ssr word as key to ssr_words hash with ssr as key and # as value
+#add additional ssr words for this gene as encountered (if Gene exists)
+sub pop_locus_hashes($)
+{
+    my $line;
+    my %local_hash;
+    
+    open(SSR_FILE, $_[0]) or die("Could not open $_[0]"); 
+        
+    while (<SSR_FILE>)
+    {
+        $line = $_;
+        chomp $line;
+        my @line_ary = split('\t',$line);
+        my $locus_id = $line_ary[0];
+        my $ssr_word = $line_ary[3];
+        my $ssr_word_count = $line_ary[4];
+        
+        # add new gene to hash value (array) for old gene hash key
+        $local_hash{$locus_id}{"ssr_words"}{$ssr_word} = $ssr_word_count;
+    }
+    
+    close SSR_FILE;
+    
+    #print "[Current Hash: " . $_[0] . "]\n";
+    #print Dumper(\%local_hash) . "\n\n";
+    #print "\n";
+    
+    return %local_hash
+}
+
+
+    #Does this locus already exist?
+#    if (!exists $esp{$locus_id})
+#    {
+
+
+
+
+#Read blastall results
+#foreach line splits on tab get 1st gene identifier
+    #look in spain hash for gene id
+        #look at each ssr_words key
+
+#look in greece hash for greece (2nd gene identifier)
+                #look in its ssr_words for current spain ssr_word key
+                #if present
+
+        #look in corvallis hash for corvallis (3rd gene identifier)
+                    #look in its ssr_words for current spain ssr_word key
+                    #if present
+                        #print 1st 2nd 3rd gene ids current spain ssr_word key current spain greece corvallis ssr_word{key} values (one for each separate key - i.e. corvallis_key)
+                        
+sub stitch_ssr_to_ortho()
+{
+    my $line;
+    
+    open(ORTHO_FILE, $ortho) or die("Could not open $ortho"); 
+    
+    while (<ORTHO_FILE>)
+    {
+        $line = $_;
+        chomp $line;
+        my @line_ary = split('\t',$line);
+        my $cor_locus = $line_ary[0];
+        my $esp_locus = $line_ary[1];
+        my $gre_locus = $line_ary[2];
+        
+        #print "$cor_locus\t$esp_locus\t$gre_locus\n";
+        
+        if (exists $esp{$esp_locus})
+        {
+            foreach my $curr_esp_ssr_word (keys $esp{$esp_locus}{ssr_words}) {
+                #print "$esp_locus : $curr_esp_ssr_word: " . $esp{$esp_locus}{ssr_words}{$curr_esp_ssr_word} . "\n";
+                if (exists $gre{$gre_locus})
+                {
+                    foreach my $curr_gre_ssr_word (keys $gre{$gre_locus}{ssr_words}) {
+                        if ($curr_esp_ssr_word eq $curr_gre_ssr_word) {
+                            #print "$esp_locus:$curr_esp_ssr_word:" . $esp{$esp_locus}{ssr_words}{$curr_esp_ssr_word}
+                            #    . "\t$gre_locus:$curr_gre_ssr_word:" . $gre{$gre_locus}{ssr_words}{$curr_gre_ssr_word} . "\n";
+                            if (exists $cor{$cor_locus})
+                            {
+                                foreach my $curr_cor_ssr_word (keys $cor{$cor_locus}{ssr_words}) {
+                                    if ($curr_esp_ssr_word eq $curr_cor_ssr_word) {
+                                        if (($esp{$esp_locus}{ssr_words}{$curr_esp_ssr_word} != $gre{$gre_locus}{ssr_words}{$curr_gre_ssr_word}) 
+                                            || ($esp{$esp_locus}{ssr_words}{$curr_esp_ssr_word} != $cor{$cor_locus}{ssr_words}{$curr_cor_ssr_word})
+                                            || ($gre{$gre_locus}{ssr_words}{$curr_gre_ssr_word} != $cor{$cor_locus}{ssr_words}{$curr_cor_ssr_word}))
+                                        {
+                                            if ((length($curr_esp_ssr_word) > 2)) { # dimer exclusion
+                                                print "$curr_esp_ssr_word"
+                                                    . "\t$esp_locus\t$esp{$esp_locus}{ssr_words}{$curr_esp_ssr_word}"
+                                                    . "\t$gre_locus\t$gre{$gre_locus}{ssr_words}{$curr_gre_ssr_word}"
+                                                    . "\t$cor_locus\t$cor{$cor_locus}{ssr_words}{$curr_cor_ssr_word}\n";
+                                            }
+                                            #print "$esp_locus:$curr_esp_ssr_word:" . $esp{$esp_locus}{ssr_words}{$curr_esp_ssr_word}
+                                            #    . "\t$gre_locus:$curr_gre_ssr_word:" . $gre{$gre_locus}{ssr_words}{$curr_gre_ssr_word}
+                                            #    . "\t$cor_locus:$curr_cor_ssr_word:" . $cor{$cor_locus}{ssr_words}{$curr_cor_ssr_word} . "\n";
+                                        }
+                                    }
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        }
+        #print "\n";
+    }
+    close ORTHO_FILE;
+}
+                        
+                        
+# main
+%esp = pop_locus_hashes($esp_ssr);
+%gre = pop_locus_hashes($gre_ssr);
+%cor = pop_locus_hashes($cor_ssr);
+
+stitch_ssr_to_ortho();
+
+exit;