#!/usr/bin/perl
+#########################################################
+# Written by Justin Elser 4/29/2009 #
+# #
+# This program takes the genes known to interact #
+# in the long day flowering process in #
+# Arabidopsis and predicts the similar short day #
+# interaction in rice #
+# #
+# Uses the orthologs first, then paralogs #
+# #
+#########################################################
+
+
+use strict;
+use warnings;
+
+# print usage
+if ($#ARGV !=4) {
+ print "usage: flowering_interaction.pl input_file interaction_network_file ortholog_file paralog_file output_file_prefix\n";
+ exit;
+}
+
+my $in_file = $ARGV[0];
+my $inter_file = $ARGV[1];
+my $ortho_file = $ARGV[2];
+my $para_file = $ARGV[3];
+my $out_file = $ARGV[4] . ".sif";
+my $out_file_inter = $ARGV[4] . "_inter.sif";
+my $out_file_ortho = $ARGV[4] . "_ortho.sif";
+my $out_file_para = $ARGV[4] . "_para.sif";
+
+my %in_hash;
+
+
+open (input_file, "$in_file") || die "Error: file '$in_file' can not be opened \n";
+while(<input_file>) {
+ my $entry = $_;
+ # strip off newline characters
+ $entry =~ s/\r//g;
+ $entry =~ s/\n//g;
+ # split the columns into 2 separate variables (using either multiple congruent spaces or a tab)
+ my ($gene_name, $gene_id) = split /\s{2,}|\t/, $entry;
+ $in_hash{$gene_id} = $gene_name;
+}
+close (input_file);
+
+open (interaction_file, "$inter_file") || die "Error: file '$inter_file' can not be opened\n";
+my %inter_hash;
+while(<interaction_file>) {
+ my $entry = $_;
+ # strip off newline characters
+ $entry =~ s/\r//g;
+ $entry =~ s/\n//g;
+ # split the columns into 3 separate variables
+ my ($gene_1, $inter_type, $gene_2) = split ("\t", $entry);
+ # change gene ids to all caps (for matching)
+ $gene_1 =~ tr/a-z/A-Z/;
+ $gene_2 =~ tr/a-z/A-Z/;
+
+ # because it doesn't matter which way the interaction goes, need to do the interaction in both directions
+ # ie. as gene_1 as the key then as gene_2 as the key
+ if(defined($inter_hash{$gene_1})){
+ # if gene already in hash, just add to the list
+ my $oldhash = $inter_hash{$gene_1};
+ $oldhash->{'type'} = "$oldhash->{'type'}\t$inter_type";
+ $oldhash->{'inter_gene'} = "$oldhash->{'inter_gene'}\t$gene_2";
+ $inter_hash{$gene_1} = $oldhash;
+ # if new gene, create hash element
+ }else{
+ my %hash;
+ $hash{'map_gene'} = $gene_1;
+ $hash{'type'} = $inter_type;
+ $hash{'inter_gene'} = $gene_2;
+ $inter_hash{$gene_1} = \%hash;
+ }
+
+ if(defined($inter_hash{$gene_2})){
+ # if new gene in the hash, just add to the list
+ my $oldhash = $inter_hash{$gene_2};
+ $oldhash->{'type'} = "$oldhash->{'type'}\t$inter_type";
+ $oldhash->{'inter_gene'} = "$oldhash->{'inter_gene'}\t$gene_1";
+ $inter_hash{$gene_2} = $oldhash;
+ # if new gene, create hash element
+ }else{
+ my %hash;
+ $hash{'map_gene'} = $gene_2;
+ $hash{'type'} = $inter_type;
+ $hash{'inter_gene'} = $gene_1;
+ $inter_hash{$gene_2} = \%hash;
+ }
+}
+close(interaction_file);
+
+
+
+my $min_ident=0;
+
+my %ortho_hash;
+#my @ortho_array;
+
+open (ortholog_file, "$ortho_file") || die "Error: file '$ortho_file' can not be opened\n";
+while(<ortholog_file>) {
+ my $entry = $_;
+ # strip off newline characters
+ $entry =~ s/\r//g;
+ $entry =~ s/\n//g;
+ # split the columns into 3 separate variables
+ my ($gene_id, $ortho_id, $ident_id) = split("\t", $entry);
+ # change gene ids to all caps
+ $gene_id =~ tr/a-z/A-Z/;
+ $ortho_id =~ tr/a-z/A-Z/;
+ # strip off the TAIR-G suffix on ids
+ $gene_id =~ s/\-TAIR-G//g;
+
+ # check to make sure the %identity is above the minimum defined above
+ if($ident_id =~ /\d/ && $ident_id>=$min_ident){
+ # if gene_id already found, add the new ortholog to hash
+ if(defined($ortho_hash{$gene_id})){
+ my $oldhash = $ortho_hash{$gene_id};
+ $oldhash->{'ortho'} = "$oldhash->{'ortho'}\t$ortho_id";;
+ $ortho_hash{$gene_id} = $oldhash;
+ # if new gene_id, create hash element
+ }else{
+ my %hash;
+ $hash{'ortho'} = $ortho_id;
+ $hash{'gene'} = $gene_id;
+ $ortho_hash{$gene_id} = \%hash;
+ #push @ortho_array, $gene_id;
+ }
+ }
+}
+close (ortholog_file);
+
+my %para_hash;
+open(paralog_file, "$para_file") || die "Error: file '$para_file' can not be opened\n";
+
+ my $min_ident_para = 0; # set the threshold for paralog identities
+ while(<paralog_file>) {
+ my $entry = $_;
+ # strip off newline characters
+ $entry =~ s/\r//g;
+ $entry =~ s/\n//g;
+ # split the columns into 3 separate variables
+ my ($gene_1, $gene_2, $ident) = split("\t", $entry);
+ # skip if $ident is empty or Nan
+ next if(!defined($ident));
+ next if($ident =~ /D/);
+ next if($ident eq "");
+ next if($ident =~ /\%/);
+ # change gene ids to all caps
+ $gene_1 =~ tr/a-z/A-Z/;
+ $gene_2 =~ tr/a-z/A-Z/;
+
+ # put the genes in ASCII order to help remove dupes
+ if($gene_1 gt $gene_2) {
+ my $temp = $gene_1;
+ $gene_1 = $gene_2;
+ $gene_2 = $temp;
+ }
+
+ # only use paralogs with high confidence values
+ if($ident>=$min_ident_para) {
+ # most genes will show up many times, so push values for hash key
+ if(defined($para_hash{$gene_1})) {
+ my $oldhash = $para_hash{$gene_1};
+ $oldhash->{'gene2'} = "$oldhash->{'gene2'}\t$gene_2";;
+ $para_hash{$gene_1} = $oldhash;
+ #print "$oldhash\n";
+ }else{
+ my %hash;
+ $hash{'gene1'} = $gene_1;
+ $hash{'gene2'} = $gene_2;
+ $para_hash{$gene_1} = \%hash;
+ }
+ }
+
+ }
+
+ close(paralog_file);
+
+# open output files for writing
+open(output_file, ">$out_file");
+open(output_file_inter, ">$out_file_inter");
+open(output_file_ortho, ">$out_file_ortho");
+open(output_file_para, ">$out_file_para");
+
+
+
+# initialize the counters
+my $Ath_inter_count = 0;
+my $rice_ortho_count = 0;
+my $rice_para_count = 0;
+
+foreach my $key (keys %in_hash) {
+ my $name = $in_hash{$key};
+
+ # find all interactions with the genes in %in_hash
+ if(defined($inter_hash{$key})) {
+
+ my @inter_array = split ("\t", $inter_hash{$key}->{'inter_gene'});
+ my @inter_type_array = split ("\t", $inter_hash{$key}->{'type'});
+ my $inter_index = @inter_type_array;
+ for (my $i=0; $i<$inter_index; $i++) {
+ my $in_gene_1 = $key;
+ my $in_gene_2 = $inter_array[$i];
+ # add one to the number of Ath interactions counted
+ $Ath_inter_count++;
+ # output the interactions to file
+ print output_file_inter "$in_gene_1\t$inter_type_array[$i]\t$in_gene_2\n";
+
+ # make the genes be listed in ASCII order to make sorting out dupes easier
+ if ($in_gene_1 gt $in_gene_2) { # note that this should not be used if order matters for interaction type
+ my $temp = $in_gene_1;
+ $in_gene_1 = $in_gene_2;
+ $in_gene_2 = $temp;
+ }
+
+ # next step is to find all the orthologs for both genes in the interaction
+ if(exists($ortho_hash{$in_gene_2})) {
+ my @ortho_gene_2_array = split ("\t", $ortho_hash{$in_gene_2}->{'ortho'});
+ foreach my $ortho_gene_2 (@ortho_gene_2_array) {
+ # output orthologs to file
+ print output_file_ortho "$in_gene_2\tortho\t$ortho_gene_2\n";
+
+ if(exists($ortho_hash{$in_gene_1})) {
+ my @ortho_gene_1_array = split ("\t", $ortho_hash{$in_gene_1}->{'ortho'});
+ foreach my $ortho_gene_1 (@ortho_gene_1_array) {
+ #print output_file "$ortho_gene_1\t$inter_type_array[$i]\t$ortho_gene_2\n";
+ print output_file "$ortho_gene_1\tortho\t$ortho_gene_2\n";
+ # add one to the number of orthologs counted
+ $rice_ortho_count++;
+ # output the orthologs to file
+ print output_file_ortho "$in_gene_1\tortho\t$ortho_gene_1\n";
+
+ # now find all paralogs to the orthologs found
+ if(exists($para_hash{$ortho_gene_1})) {
+ my @para_gene_1_array = split ("\t", $para_hash{$ortho_gene_1}->{'gene2'});
+ foreach my $para_gene_1 (@para_gene_1_array) {
+ # output the paralogs to file
+ print output_file_para "$ortho_gene_1\tpara\t$para_gene_1\n";
+
+ if(exists($para_hash{$ortho_gene_2})) {
+ my @para_gene_2_array = split ("\t", $para_hash{$ortho_gene_2}->{'gene2'});
+ foreach my $para_gene_2 (@para_gene_2_array) {
+ # add one to the number of paralogs counted
+ $rice_para_count++;
+ #print output_file "$para_gene_1\t$inter_type_array[$i]\t$para_gene_2\n";
+ print output_file "$para_gene_1\tpara\t$para_gene_2\n";
+ # output the paralogs to file
+ print output_file_para "$ortho_gene_2\tpara\t$para_gene_2\n";
+
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ }
+ }
+}
+
+close(output_file);
+print "Ath_inter_count = $Ath_inter_count\nrice_ortho_count = $rice_ortho_count\nrice_para_count = $rice_para_count\n";
+print "Now removing duplicates\n";
+# sort the file and get rid of duplicates
+# Note: this requires replacing the file, hence the mv command
+system "sort $out_file | uniq > $out_file.tmp; mv $out_file.tmp $out_file";
+
+
+close(output_file_inter);
+close(output_file_ortho);
+close(output_file_para);
+
+
+
--- /dev/null
+#!/usr/bin/perl
+
+use warnings;
+use strict;
+
+use DBI;
+use Term::Screen::ReadLine;
+
+if ($#ARGV != 0) {
+ print "usage: inparanoid_orthologs.pl output_file\n";
+ exit;
+}
+open(outfile,">$ARGV[0]") || die "Error: file '$ARGV[0]' can not be opened\n";
+
+# define the database handle to be used
+
+my $screen = Term::Screen::ReadLine->new();
+ # clear the screen
+ $screen->clrscr;
+ # ask for username
+ $screen->at(0,0)->puts("Username: ");
+ my $username = $screen->readline(ROW => 0, COL=>11);
+
+ # ask for password, replace character presses with stars
+ $screen->at(1,0)->puts("Password: ");
+ my $password = $screen->readline(ROW => 1, COL => 11, PASSWORD => 1);
+
+ $screen->at(2,0);
+ undef $screen;
+
+my $dbh = DBI->connect('DBI:mysql:inparanoid_data;host=floret.cgrb.oregonstate.edu', $username, $password,
+ { RaiseError=> 1, AutoCommit=>1 }
+ ) or die "Failed to connect to database: $DBI::errstr";
+
+my @species = ("Maize", "Oryza_sativa", "Ath", "Sorghum", "Brachy");
+my $num_species = @species;
+
+for (my $i=0; $i<$num_species-1; $i++) {
+ for (my $j=$i+1; $j<$num_species; $j++) {
+ # hashes to store the paralogs and orthologs
+ my (%species_1_gene_hash, %species_2_gene_hash);
+
+ # make sure the species are listed in alphabetical order to get correct table names
+ my $species_1 = $species[$i];
+ my $species_2 = $species[$j];
+ if ($species_1 lt $species_2) {
+ $species_1 = $species_1;
+ $species_2 = $species_2;
+ } else {
+ my $spec_temp = $species_1;
+ $species_1 = $species_2;
+ $species_2 = $spec_temp;
+ }
+
+ my $spec_table = "$species_1" . "_" . "$species_2";
+ my $safe_species_table = $dbh->quote_identifier($spec_table);
+ my $sth = $dbh->prepare("select * from $safe_species_table");
+
+ my $id_prev = "";
+
+ $sth->execute();
+
+ while (my @line = $sth->fetchrow_array()) {
+ my ($id, $bit_score, $spec, $score, $gene) = @line;
+ if ($id ne $id_prev) {
+ if ($spec eq $species_1) {
+ $species_1_gene_hash{$id} = $gene;
+ }else {
+ $species_2_gene_hash{$id} = $gene;
+ }
+ }else {
+ if ($spec eq $species_1) {
+ if(defined($species_1_gene_hash{$id})) {
+ $species_1_gene_hash{$id} = "$species_1_gene_hash{$id} $gene";
+ } else {
+ $species_1_gene_hash{$id} = $gene;
+ }
+ }else {
+ if(defined($species_2_gene_hash{$id})) {
+ $species_2_gene_hash{$id} = "$species_2_gene_hash{$id} $gene";
+ } else {
+ $species_2_gene_hash{$id} = $gene;
+ }
+ }
+ }
+ $id_prev = $id;
+ }
+
+ foreach my $key (keys %species_1_gene_hash) {
+ if(defined($species_2_gene_hash{$key})) {
+ print outfile "$species_1_gene_hash{$key}\t$species_2_gene_hash{$key}\n";
+ }
+ }
+ $sth->finish();
+ }
+}
+
+close(outfile);
+
#!/usr/bin/perl
+###############################################################
+# Justin Elser (elserj@science.oregonstate.edu) #
+# Parses the output from an inparanoid run and #
+# enters it into a database #
+# #
+# Version 1.00 - September 2009 #
+# Seems to work fine #
+# Version 1.01 - Nov 4 '09 #
+# Added support for strawberry #
+# #
+###############################################################
+
+
use strict;
use warnings;
$clust_id = "$species_1"."___".$species_2."___".$clust_id;
$species = find_species($species);
+ my $gene = find_gene($gene_header,$species);
+
+ # skip isomers that are not .1
+ next if ($gene =~ /\.[2-9]$/);
if(!defined($id_hash{$clust_id})) {
if ($clust_id ne $clust_id_prev) {
$id = $id_hash{$clust_id};
}
- my $gene = find_gene($gene_header,$species);
+
$sth->execute($id, $bit_score, $species, $score, $gene);
$clust_id_prev = $clust_id;
$temp = "Danio";
}elsif ($temp =~ /E\_coli/) {
$temp = "E_coli";
+ }elsif ($temp =~ /Fragaria/) {
+ $temp = "Fragaria";
}elsif ($temp =~ /Glycine/) {
$temp = "Soy";
}elsif ($temp =~ /Homo\_sapiens/) {
my $species = $_[1];
my $gene;
if ($species eq "Ath") {
- my ($name,$gene_id,$chrom,$isomer) = split("\|", $gene_header);
+ my ($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("\|", $gene_header);
+ my ($gene_id,$temp) = split(/\|/, $gene_header);
$gene = $gene_id; #???
}elsif ($species eq "Chlamy") {
- my ($name,$locus_id,$scaff_id,$temp) = split("\|",$gene_header);
+ my ($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("\|",$gene_header);
+ my ($name,$locus_id,$scaff_id,$isomer) = split(/\|/,$gene_header);
$gene = $isomer;
}elsif ($species eq "Human") {
$gene = $gene_header;
}elsif ($species eq "Neurospora") {
$gene = $gene_header;
}elsif ($species eq "Oryza_sativa") {
- my ($isomer,$temp,$type) = split("\|",$gene_header);
+ my ($isomer,$temp,$type) = split(/\|/,$gene_header);
$gene = $isomer;
}elsif ($species eq "Physcomitreall") {
- my ($name,$locus_id,$chrom_id,$prot_id) = split("\|",$gene_header);
+ my ($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("\|",$gene_header);
+ my ($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("\|",$gene_header);
+ my ($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("\|",$gene_header);
+ my ($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("\|",$gene_header);
+ my ($name,$gene_id,$chrom_id,$id) = split(/\|/,$gene_header);
$gene = $gene_id; #???
}else {
die "Error: Gene id can not be found!";
--- /dev/null
+#!/usr/bin/perl
+
+use warnings;
+use strict;
+
+use DBI;
+use Term::Screen::ReadLine;
+
+
+# define the database handle to be used
+
+my $screen = Term::Screen::ReadLine->new();
+ # clear the screen
+ $screen->clrscr;
+ # ask for username
+ $screen->at(0,0)->puts("Username: ");
+ my $username = $screen->readline(ROW => 0, COL=>11);
+
+ # ask for password, replace character presses with stars
+ $screen->at(1,0)->puts("Password: ");
+ my $password = $screen->readline(ROW => 1, COL => 11, PASSWORD => 1);
+
+ $screen->at(2,0);
+ undef $screen;
+
+my $dbh = DBI->connect('DBI:mysql:inparanoid_data;host=floret.cgrb.oregonstate.edu', $username, $password,
+ { RaiseError=> 1, AutoCommit=>1 }
+ ) or die "Failed to connect to database: $DBI::errstr";
+
+
+#### Note to self ####
+## To not have multiple values in mysql table, use insert ignore instead of insert. Or use replace.
+### also note that for insert ignore to work, must have a "unique" field
+
+# make the new table to hold the super clusters
+my $super_table = "super_clust";
+my $safe_super_table = $dbh->quote_identifier($super_table);
+
+$dbh->do("drop table if exists $safe_super_table");
+$dbh->do("CREATE TABLE $safe_super_table (
+ `super_id` INT( 11 ) NOT NULL ,
+ `species` VARCHAR( 255 ) NOT NULL ,
+ `gene` VARCHAR( 255 ) NOT NULL ,
+ UNIQUE ( `gene` )
+ ) TYPE = MYISAM");
+my $insert_sth = $dbh->prepare("insert ignore into $safe_super_table (super_id, species, gene) values (?,?,?)");
+
+my $super_id = 0; #initialize the super cluster id
+my %super_hash;
+
+#my @species = ("Maize", "Oryza_sativa", "Ath", "Sorghum", "Brachy");
+#my @species = ("Maize", "Oryza_sativa", "Ath");
+my @species = ("Ath", "Brachy", "C_elegans", "Chlamy", "Danio", "E_coli", "Fragaria", "Glycine", "Human", "Maize", "Mouse", "Neurospora", "Oryza_sativa", "Physcomitreall", "Poplar", "Sacc_cerevisiae", "Sacc_pombe", "Selaginella", "Sorghum", "Synechosystis", "Vitis_vinifera");
+my $num_species = @species;
+
+my %species_hash;
+
+for (my $i=0; $i<$num_species-1; $i++) {
+ for (my $j=$i+1; $j<$num_species; $j++) {
+ # hashes to store the paralogs and orthologs
+ my (%species_1_gene_hash, %species_2_gene_hash);
+
+ # make sure the species are listed in alphabetical order to get correct table names
+ my $species_1 = $species[$i];
+ my $species_2 = $species[$j];
+ if ($species_1 lt $species_2) {
+ $species_1 = $species_1;
+ $species_2 = $species_2;
+ } else {
+ my $spec_temp = $species_1;
+ $species_1 = $species_2;
+ $species_2 = $spec_temp;
+ }
+
+ if ($species_1 eq "Glycine") {
+ $species_1 = "Soy";
+ }
+
+ if ($species_2 eq "Glycine") {
+ $species_2 = "Soy";
+ }
+
+ if ($species_1 eq "Vitis_vinifera") {
+ $species_1 = "Grape";
+ }
+
+ if ($species_2 eq "Vitis_vinifera") {
+ $species_2 = "Grape";
+ }
+
+
+ my $spec_table = "$species_1" . "_" . "$species_2";
+ my $safe_species_table = $dbh->quote_identifier($spec_table);
+ my $sth = $dbh->prepare("select * from $safe_species_table");
+
+ my $id_prev = "";
+
+ my $rv = $sth->execute();
+
+ # error handling, make sure the table exists
+ if (!$rv) {
+ next;
+ }
+
+ while (my @line = $sth->fetchrow_array()) {
+ my ($id, $bit_score, $spec, $score, $gene) = @line;
+ if ($id ne $id_prev) {
+ if ($spec eq $species_1) {
+ $species_1_gene_hash{$id} = $gene;
+ }else {
+ $species_2_gene_hash{$id} = $gene;
+ }
+ }else {
+ if ($spec eq $species_1) {
+ if(defined($species_1_gene_hash{$id})) {
+ $species_1_gene_hash{$id} = "$species_1_gene_hash{$id} $gene";
+ } else {
+ $species_1_gene_hash{$id} = $gene;
+ }
+ }else {
+ if(defined($species_2_gene_hash{$id})) {
+ $species_2_gene_hash{$id} = "$species_2_gene_hash{$id} $gene";
+ } else {
+ $species_2_gene_hash{$id} = $gene;
+ }
+ }
+ }
+ $id_prev = $id;
+ }
+ $sth->finish();
+
+ # Each key defines a species pair cluster
+ foreach my $key (keys %species_1_gene_hash) {
+ if(defined($species_2_gene_hash{$key})) {
+ my (@spec_1_array, @spec_2_array);
+ @spec_1_array = split " ", $species_1_gene_hash{$key};
+ @spec_2_array = split " ", $species_2_gene_hash{$key};
+
+ # if the gene is already in a cluster, use its id #
+ my $super_temp_id;
+
+ foreach my $super_gene (@spec_1_array) {
+ if(defined($super_hash{$super_gene})) {
+ $super_temp_id = $super_hash{$super_gene};
+ last;
+ }
+ }
+
+ if(!defined($super_temp_id)) {
+ foreach my $super_gene (@spec_2_array) {
+ if(defined($super_hash{$super_gene})) {
+ $super_temp_id = $super_hash{$super_gene};
+ last;
+ }
+ }
+ }
+
+ # if none of the genes are in a cluster already, get a new id #
+ if(!defined($super_temp_id)) {
+ ++$super_id;
+ $super_temp_id = $super_id;
+ }
+
+ # build the hash and put the entries in the database
+ foreach my $super_gene (@spec_1_array) {
+ $super_hash{$super_gene} = $super_temp_id;
+ $insert_sth->execute($super_temp_id,$species_1,$super_gene);
+ }
+ foreach my $super_gene (@spec_2_array) {
+ $super_hash{$super_gene} = $super_temp_id;
+ $insert_sth->execute($super_temp_id,$species_2,$super_gene);
+ }
+
+ }
+ }
+
+ }
+}
+
+
projects / old-jaiswallab-svn / .git / commitdiff