Perl script that makes a list of all families in the TreeFam mysql database

list_treefam_families.pl

#!/usr/local/bin/perl

# 
# Perl script list_treefam_families.pl
# Written by Avril Coghlan (alc@sanger.ac.uk)
# 27-Feb-07.
# Updated 6-Dec-07.  
#
# This perl script makes a list of families in the TreeFam mysql database.
#
# The command-line format is:
# % perl <list_treefam_families.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 list_treefam_families.pl\n\n";
   print "perl list_treefam_families.pl <release>\n";
   print "where <release> is the release of the TreeFam database to use.\n";
   print "For example, >perl -w list_treefam_families.pl 4\n";
   exit;
}

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

# DECLARE MYSQL USERNAME AND HOST:
use lib "/home/bcri/acoghlan/x86_64-linux-thread-multi";
use DBI;

# FIND WHICH RELEASE OF THE TREEFAM DATABASE TO USE:

$release                   = $ARGV[0];

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

# GET A LIST OF ALL TREEFAM-A FAMILIES:

$database                  = "dbi:mysql:treefam_".$release.":db.treefam.org:3308";
$dbh                       = DBI->connect("$database", 'anonymous', '') || return;
$table_w                   = 'familyA';
$st                        = "SELECT AC 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)    
   {
      $AC                  = $array[0];  
      print "$AC\n";
   }
}
$rc                        = $dbh->disconnect();
$rc                        = "";
print STDERR "Read in list of TreeFam-A families...\n";

# GET A LIST OF ALL TREEFAM-B FAMILIES:

$dbh                       = DBI->connect("$database", 'anonymous', '') || return;
$table_w                   = 'familyB';
$st                        = "SELECT AC 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)    
   {
      $AC                  = $array[0];  
      print "$AC\n";
   }
}
$rc                        = $dbh->disconnect();
$rc                        = "";
print STDERR "Read in list of TreeFam-B families...\n";

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

print STDERR "FINISHED.\n";

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