density clusters now available

Author: AdamDS

HotSpot3D-0.6.4.tar.gz renamed to HotSpot3D-1.0.0.tar.gz

@@ -7,7 +7,7 @@ Usage
 -----
 
         Program:     HotSpot3D - 3D mutation proximity analysis program.
-        Version:     V0.6.5
+        Version:     V1.0.0
          Author:     Beifang Niu, John Wallis, Adam D Scott, & Sohini Sengupta
 
   Usage: hotspot3d <command> [options]

README.md

@@ -8,7 +8,7 @@
 use strict;
 use warnings;
 
-our $VERSION = 'V0.6.5';
+our $VERSION = 'V1.0.0';
 
 use Carp;
 use FileHandle;
@@ -22,7 +22,6 @@ use TGI::Mutpro::Main::Cluster;
 use TGI::Mutpro::Main::Significance;
 use TGI::Mutpro::Main::Summary;
 use TGI::Mutpro::Main::Visual;
-use TGI::Mutpro::Main::Cluster::Density;
 use TGI::Mutpro::Preprocess::Drugport;
 use TGI::Mutpro::Preprocess::Uppro;
 use TGI::Mutpro::Preprocess::Calpro;
@@ -37,7 +36,7 @@ use TGI::Mutpro::Preprocess::AllPreprocess;
 
 my $subCmd = shift;
 ## Add module option here
-my %cmds = map{ ($_, 1) } qw( search post visual cluster sigclus summary drugport uppro calpro calroi statis anno trans homo cosmic prior prep density help );
+my %cmds = map{ ($_, 1) } qw( search post visual cluster sigclus summary drugport uppro calpro calroi statis anno trans homo cosmic prior prep help );
 unless (defined $subCmd) { die help_text(); };
 unless (exists $cmds{$subCmd}) {
     warn ' Please give valid sub command ! ', "\n";
@@ -62,7 +61,6 @@ SWITCH:{
     $subCmd eq 'cosmic'   && do { TGI::Mutpro::Preprocess::Cosmic->new();         last SWITCH; };
     $subCmd eq 'prior'    && do { TGI::Mutpro::Preprocess::Prior->new();          last SWITCH; };
     $subCmd eq 'prep'     && do { TGI::Mutpro::Preprocess::AllPreprocess->new();  last SWITCH; };
-    $subCmd eq 'density'  && do { TGI::Mutpro::Main::Cluster::Density->new();     last SWITCH; };
     $subCmd eq 'help'     && do { die help_text();                                last SWITCH; };
 }
 sub help_text {
@@ -94,7 +92,6 @@ Version: $VERSION
               sigclus   --  3) Determine significance of clusters
               summary   --  4) Summarize clusters
               visual    --  5) Visulization of 3D proximity
-              density   --  6) Determine mutation-mutation and mutation-drug density-based clusters
 
            help      --  this message
 

bin/hotspot3d

@@ -1,6 +1,6 @@
 name    = HotSpot3D
-author  = Beifang Niu, John Wallis, Adam D Scott, & Sohini Sengupta from McDonnell Genome Institute of Washington University at St. Louis
-version = 0.6.5
+author  = Beifang Niu, John Wallis, Adam D Scott, Sohini Sengupta , & Amila Weerasinghe from McDonnell Genome Institute of Washington University at St. Louis
+version = 1.0.0
 license = Perl_5
 copyright_holder = McDonnell Genome Institute at Washington University
 copyright_year   = 2013

dist.ini

@@ -87,6 +87,10 @@ sub process {
 	if ( not defined $this->{'clustering'} ) {
 		warn "HotSpot3D::Cluster warning: no clustering option given, setting to default network\n";
 	}
+	if ( $this->{'clustering'} eq $DENSITY ) {
+		TGI::Mutpro::Main::Density->new();
+		exit;
+	}
 	if ( not defined $this->{'p_value_cutoff'} ) {
 		if ( not defined $this->{'3d_distance_cutoff'} ) {
 			warn "HotSpot3D::Cluster warning: no pair distance limit given, setting to default p-value cutoff = 0.05\n";
@@ -128,10 +132,6 @@ sub process {
 		warn "Using default distance-measure = \'average\'\n";
 		$this->{'distance_measure'} = $AVERAGEDISTANCE;
 	}
-	if ( $this->{'clustering'} eq $DENSITY ) {
-		TGI::Mutpro::Main::Density->new();
-		exit;
-	}
 	if ( $this->{'vertex_type'} ne $UNIQUE ) {
 		unless( $this->{'maf_file'} ) { warn 'You must provide a .maf file if not using unique vertex type! ', "\n"; die $this->help_text(); }
 		unless( -e $this->{'maf_file'} ) { warn "The input .maf file )".$this->{'maf_file'}.") does not exist! ", "\n"; die $this->help_text(); }

lib/TGI/Mutpro/Main/Cluster.pm

@@ -1,4 +1,4 @@
-package TGI::Mutpro::Main::Cluster::Density;
+package TGI::Mutpro::Main::Density;
 
 use strict;
 use warnings;
@@ -9,6 +9,8 @@ use Data::Dumper qw(Dumper);
 use List::Util qw[min max];
 use Getopt::Long;
 
+our @ISA = qw( TGI::Mutpro::Main::Cluster );
+
 my $EPSILONDEFAULT = 4;
 my $MINPTSDEFAULT = 3;
 my $CUTOFFSTARTDEFAULT = 2;
@@ -207,4 +209,4 @@ HELP
 
 }
 
-1;
+1;