Perl script that prints out the total number of genes in families, and the total number of families, in a particular TreeFam release

treefam_release2.pl

#!/usr/local/bin/perl

# 
# Perl script treefam_release2.pl
# Written by Avril Coghlan (a.coghlan@ucc.ie)
# 10-Feb-09.
#
# This perl script prints out the total number of genes in families,
# and the total number of families, in a particular TreeFam release.
#
# The command-line format is:
# % perl <treefam_release2.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_release2.pl\n\n";
   print "perl treefam_release2.pl <release>\n";
   print "where <release> is the release of the TreeFam database to use.\n";
   print "For example, >perl -w treefam_release2.pl 7\n";
   exit;
}

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

# DECLARE MYSQL USERNAME AND HOST:
use DBI;

# FIND WHICH RELEASE OF THE TREEFAM DATABASE TO USE:

$release                   = $ARGV[0];

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

# FIND THE TOTAL NUMBER OF GENES IN FAMILIES IN THIS TREEFAM RELEASE:

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

# NOW DISCONNECT FROM THE DATABASE:

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

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

print STDERR "FINISHED.\n";

#------------------------------------------------------------------#
# FIND THE TOTAL NUMBER OF GENES IN FAMILIES IN THIS TREEFAM RELEASE:

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

   # READ IN THE GENE IDS FOR TRANSCRIPT IDS:
   $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              = $array[1];
         if ($GID{$ID}) { print STDERR "ERROR: already have GID for ID $ID\n"; exit;}
         $GID{$ID}         = $GID;
      }
   }

   # READ IN THE GENES IN FAMILIES:
   $table_w                = 'fam_genes';
   $st                     = "SELECT ID, AC from $table_w WHERE FLAG=\'FULL\'"; 
   $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];
         $AC               = $array[1];
         if ($GID{$ID}) # FOR SOME IDs IN THE fam_genes TABLE, THERE IS NO GID DEFINED IN THE
                        # genes TABLE. THIS OCCURS FOR TRANSCRIPTS IN SEED TREEFAM-A FAMILIES
                        # WHICH CAME FROM VERY OLD GENE SETS:
         {
            $GID           = $GID{$ID};
            if (!($SEEN{$GID}))
            {
               $SEEN{$GID} = 1;
               $num_genes++;
            }
         }
         if (!($SEEN_FAMILY{$AC}))
         {
            $SEEN_FAMILY{$AC} = 1;
            $num_families++;
         }
      }
   }

   print STDERR "Read in $num_genes genes in $num_families families\n";
   print "Read in $num_genes genes in $num_families families\n";
}

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