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get_gin_names.pl
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get_gin_names.pl
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#!/usr/bin/perl
# generate mapping of wbgenes to their possible names, with same names to different genes in reverse priority in @tables. 2015 15 16
use strict;
use warnings;
use DBI;
my $dbh = DBI->connect ( "dbi:Pg:dbname=testdb;host=131.215.52.76", "", "") or die "Cannot connect to database!\n"; # for remote access
# my $dbh = DBI->connect ( "dbi:Pg:dbname=wobrdb", "", "") or die "Cannot connect to database!\n";
my $result;
my %geneNameToId; my %geneIdToName;
# my @tables = qw( gin_locus );
my @tables = qw( gin_wbgene gin_seqname gin_synonyms gin_locus );
# my @tables = qw( gin_seqname gin_synonyms gin_locus );
foreach my $table (@tables) {
my $result = $dbh->prepare( "SELECT * FROM $table;" );
$result->execute();
while (my @row = $result->fetchrow()) {
my $id = "WBGene" . $row[0];
my $name = $row[1];
my ($lcname) = lc($name);
$geneIdToName{$id} = $name;
# $geneNameToId{$lcname} = $id;
$geneNameToId{$name} = $id; } }
# return (\%geneNameToId, \%geneIdToName);
my $outfile = '/home/azurebrd/cron/gin_names/gin_names.txt';
open (OUT, ">$outfile") or die "Cannot create $outfile : $!";
foreach my $name (sort { $geneNameToId{$a} cmp $geneNameToId{$b} } keys %geneNameToId) {
my $id = $geneNameToId{$name};
my $primary = '';
if ($geneIdToName{$id} eq $name) { $primary = 'primary'; }
print OUT qq($id\t$name\t$primary\n);
} # foreach my $name (sort keys %geneNameToId)
close (OUT) or die "Cannot close $outfile : $!";