Perl script to find genes that appear in more than one TreeFam-A seed tree

treefam_overlaps2.pl

#!/usr/local/bin/perl

# 
# Perl script treefam_overlaps2.pl
# Written by Avril Coghlan (alc@sanger.ac.uk).
# 25-Aug-06.  
#
# For the TreeFam project.
#
# This perl script connects to the MYSQL database of
# TreeFam families and prints out a list of the genes that
# appear in more than one TreeFam-A seed tree. This script
# uses Jean-Karim's TreeFam API.
# 
# The command-line format is:
# % perl <treefam_overlaps2.pl> 
#
#------------------------------------------------------------------#

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

$num_args                  = $#ARGV + 1;
if ($num_args != 0)
{
   print "Usage of treefam_overlaps2.pl\n\n";
   print "perl -w treefam_overlaps2.pl\n";
   print "For example, >perl -w treefam_overlaps2.pl\n";
   exit;
}

# DECLARE MYSQL USERNAME AND HOST:

use strict;
use Treefam::DBConnection;

my $VERBOSE                = 0; # IF $VERBOSE==1, PRINT OUT EXTRA DETAILS.
my $dbc                    =  Treefam::DBConnection->new();

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

my %FAMILY                 = (); # HASH TABLE TO KEEP A RECORD OF THE TREEFAM-A FAMILIES THAT A GENE IS IN.

# GET ALL THE TREEFAM-A FAMILIES IN THE CURRENT RELEASE:
my $famh                   = $dbc->get_FamilyHandle();    # GET A FAMILY HANDLE.
my @families               = $famh->get_all_by_type('A'); # GET ALL TREEFAM-A FAMILIES.
my $no_families            = 0;
foreach my $family(@families)
{
   if ($VERBOSE == 1) { print $family->ID,"\n";}
   my $AC                  = $family->ID();         # GET THE FAMILY ID.
   $no_families++;
   print STDERR "$no_families: reading family $AC...\n";
   my $tree                = $family->tree('seed'); # GET THE TREEFAM-A SEED TREE. 
   # GET THE NAMES OF ALL THE GENES IN THIS TREE:
   my @leaves              = $tree->get_leaf_nodes;
   foreach my $leaf(@leaves) 
   {
      my @tags             = $leaf->get_all_tags();
      if ($VERBOSE == 1) { print "ID: ",$leaf->id(),"\t"; } # THIS IS THE SYMBOL."_".SPECIES, eg. srb11_SCHP0 OR CCNC_HUMAN
      foreach my $tag(@tags) 
      {
         # THE TAGS ARE:
         # G: GENE ID, eg. SPBC12D12.06 OR ENSG00000112237 
         # O: TREEFAM ID. eg. SPBC12D12.06 OR ENST00000326298.2
         # S: SPECIES, eg. SCHP0 OR HUMAN
         for my $value ($leaf->get_tag_values($tag)) 
         {                
            if ($tag eq 'G')
            {
               my $GID        = $value;
               if ($VERBOSE == 1) { print "gene $GID (AC $AC)\n";}
               # REMEMBER THE FAMILIES THAT THIS GENE IS IN:
               if (!($FAMILY{$GID})) { $FAMILY{$GID} = $AC;                  }
               else                  { $FAMILY{$GID} = $FAMILY{$GID}.",".$AC;}
            }
         }           
      }
   }
}
if ($VERBOSE == 1) { print "\n\n";}

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

# PRINT OUT A LIST OF THE GENES THAT APPEAR IN TREEFAM-A SEED FAMILIES, AND THE
# FAMILIES THAT THEY APPEAR IN:

print "GENE NUMBER_OF_FAMILIES FAMILIES\n";

my $no_overlapping_families   = 0;
my $no_genes                  = 0;
my %SEEN                      = ();
foreach my $GID (keys %FAMILY)
{
   my $family                 = $FAMILY{$GID};
   my @family                 = split(/\,/,$family); # THIS IS A LIST OF THE FAMILIES THAT A GENE APPEARS IN.
   my $no_families            = $#family + 1;        # THIS IS THE NUMBER OF FAMILIES THAT A GENE APPEARS IN.
   if ($no_families > 1)
   {
      if ($SEEN{$GID}) { print STDERR "ERROR: already counted gene $GID.\n"; exit;}
      $SEEN{$GID}             = 1;
      $no_genes++;
      print "$GID $no_families $family\n"; 

      # CHECK IF WE HAVE SEEN THESE FAMILIES BEFORE:
      for (my $i = 0; $i < $no_families; $i++)
      {
         my $this_family      = $family[$i];
         if (!($SEEN{$this_family})) 
         { 
            $no_overlapping_families++; 
            $SEEN{$this_family} = 1; 
         }
     } 
   }
}
print "There are $no_genes genes in more than one TreeFam-A seed family.\n";
print "They are in $no_overlapping_families different TreeFam-A seed families.\n";

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

print STDERR "FINISHED.\n";