Perl script that prints out all the genes in a particular TreeFam family.

treefam_4_genes.pl

#!/usr/local/bin/perl

# 
# Perl script treefam_4_genes.pl 
# Written by Avril Coghlan (alc@sanger.ac.uk)
# 31-Oct-07.
#
# For the TreeFam project.
#
# This perl script prints out all the genes in a TreeFam-4 family.
#
# The command-line format is:
# % perl <treefam_4_genes.pl> family
# where family is the family identifier.
#
#------------------------------------------------------------------#

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

$num_args                  = $#ARGV + 1;
if ($num_args != 1)
{
   print "Usage of treefam_4_genes.pl\n\n";
   print "perl treefam_4_genes.pl <family>\n";
   print "where <family> is the family identifier.\n";
   print "For example, >perl -w treefam_4_genes.pl TF101073\n";
   exit;
}

# READ IN MY PERL MODULES:

BEGIN {
    unshift (@INC, '/nfs/team71/phd/alc/perl/modules');
}

use lib "/nfs/team71/phd/alc/perl/treefam/Treefam_api_3may07/"; 
use DBI;
use Treefam::DBConnection;

# FIND THE NAME OF THE INPUT FAMILY:

$family_id                 = $ARGV[0];

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

# GET ALL THE GENES IN THIS FAMILY:

$dbc                       =  Treefam::DBConnection->new();
$famh                      = $dbc->get_FamilyHandle();
$family                    = $famh->get_by_id($family_id);
if (!(defined($family)))
{
  print "Do not have $family_id in the database...\n";
  exit;
}

my $tree                   = $family->get_tree('clean'); 
# FIRST PRINT ALL THE GENES IN THE FAMILY:
my @leaves                 = $tree->get_leaves;
foreach my $leaf(@leaves)
{
   if (defined($leaf->sequence_id())) # FOR SOME LEAVES, WE DON'T SEE TO HAVE 
   # A SEQUENCE ID, eg. SEE RICE GENE IN http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF101025
   {
      my $id               = $leaf->sequence_id();
      # GET THE ENSEMBL/ORIGINAL GENE NAME:
      my $gene_handle      = $dbc->get_GeneHandle();
      if (defined($gene_handle->get_by_sequence_id($id))) { $gene =  $gene_handle->get_by_sequence_id($id);}
      else { print STDERR "ERROR: cannot get gene for id $id\n"; exit;                                     }
      if (defined($gene->ID)) { $gene_id = $gene->ID;}
      else                    { $gene_id = "unknown";}
      print "HAVE GENE $gene_id\n";
   }
}

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

print STDERR "FINISHED.\n";