Perl script that finds cases where different alternative spliceforms of the same gene do not have unique transcript ids in the 'genes' table of the TreeFam mysql database

treefam_QC7.pl

#!/usr/local/bin/perl

# 
# Perl script treefam_QC7.pl
# Written by Avril Coghlan (a.coghlan@ucc.ie)
# 4-Feb-09.
#
# This perl script finds cases where more different alternative splices of
# the same gene do not have unique transcript ids in the 'genes' table.
#
# The command-line format is:
# % perl <treefam_QC7.pl> <release> 
#   where <release> is the release of the TreeFam database to use.
#
#
#------------------------------------------------------------------#

# CHECK IF THERE ARE THE CORRECT NUMBER OF COMMAND-LINE ARGUMENTS:

$num_args                  = $#ARGV + 1;
if ($num_args != 1)
{
   print "Usage of treefam_QC7.pl\n\n";
   print "perl treefam_QC7.pl <release>\n";
   print "where <release> is the release of the TreeFam database to use.\n";
   print "For example, >perl -w treefam_QC7.pl 7\n";
   exit;
}

#------------------------------------------------------------------#

# DECLARE MYSQL USERNAME AND HOST:
use DBI;

# FIND WHICH RELEASE OF THE TREEFAM DATABASE TO USE:

$release                   = $ARGV[0];

$VERBOSE                   = 1;

#------------------------------------------------------------------#

$database                  = "dbi:mysql:treefam_".$release.":db.treefam.org:3308";
$dbh                       = DBI->connect("$database", 'anonymous', '') || return;

# READ IN THE GENE ID FOR EVERY TRANSCRIPT ID, AND CHECK THAT EACH
# TRANSCRIPT HAS A UNIQUE TRANSCRIPT ID:

&read_geneids($dbh);

# NOW DISCONNECT FROM THE DATABASE:

$rc                        = $dbh->disconnect();
$rc                        = "";

#------------------------------------------------------------------#

print STDERR "FINISHED.\n";

#------------------------------------------------------------------#

# READ THE GENE ID FOR EVERY TRANSCRIPT ID, AND CHECK THAT EACH TRANSCRIPT
# HAS A UNIQUE TRANSCRIPT ID:

sub read_geneids
{
   my $dbh                 = $_[0];
   my $table_w;
   my $st;
   my $sth;
   my $rv;
   my @array;
   my $ID;
   my $GID;
   my %SEEN                = ();

   $table_w                = 'genes';
   $st                     = "SELECT ID, GID from $table_w";
   $sth                    = $dbh->prepare($st) or die "Cannot prepare $st: $dbh->errstr\n";
   $rv                     = $sth->execute or die "Cannot execute the query: $sth->errstr";
   if ($rv >= 1)
   {
      while ((@array) = $sth->fetchrow_array)
      {
         $ID               = $array[0];
         $GID              = $array[1];
         if (!($SEEN{$ID}))
         {
            $SEEN{$ID}     = 1;
         } 
         else
         {
            print "WARNING: id $ID (gene $GID) is not unique in the genes table\n";
         }
      }
   }

   print STDERR "Read in gene ids\n";
   print "Read in gene ids\n";
}

#------------------------------------------------------------------#