Perl script that gets the TreeFam clean tree for a family.

get_trees2.pl

#!/usr/local/bin/perl

# 
# Perl script get_trees2.pl
# Written by Avril Coghlan (alc@sanger.ac.uk)
# 6-Mar-07.  
# Updated 6-Dec-07.
#
# For the TreeFam project.
#
# This perl script gets the TreeFam clean tree for a family.
#
# The command-line format is:
# % perl <get_trees2.pl> family
# where family is the TreeFam family of interest.
#
#------------------------------------------------------------------#

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

$num_args                  = $#ARGV + 1;
if ($num_args != 1)
{
   print "Usage of get_trees2.pl\n\n";
   print "perl get_trees2.pl <family>\n";
   print "where <family> is the TreeFam family of interest.\n";
   print "For example, >perl get_trees2.pl TF101001\n";
   exit;
}

use DBI;

# FIND THE NAME OF THE FAMILY:     

$family                    = $ARGV[0];

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

# CONNECT TO THE MYSQL DATABASE:
$dbh                       = DBI->connect("dbi:mysql:treefam_7:db.treefam.org:3308", 'anonymous', '') || return;
$table_w                   = "trees";

# READ IN THE INPUT LIST:

print STDERR "Getting clean tree for $family...\n";
$found_tree          = 0;
$st                  = "SELECT TREE, TYPE from $table_w WHERE AC=?";
$sth                 = $dbh->prepare($st) or die "Cannot prepare $st: $dbh->errstr\n";
$rv                  = $sth->execute($family) or die "Cannot execute the query: $sth->errstr";
if ($rv >= 1)
{
   while ((@array) = $sth->fetchrow_array)
  {
       $the_tree      = $array[0];
       $type          = $array[1];
       if ($type eq 'CLEAN')
       {
           print "$the_tree\n";
           $found_tree = 1;
        }
  }
}
if ($found_tree == 0) { print STDERR "WARNING: did not find clean tree for $family\n";}

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

print STDERR "FINISHED.\n";