clusters ready for density

Author: AdamDS

HotSpot3D-0.6.4.tar.gz

@@ -7,7 +7,7 @@ Usage
 -----
 
         Program:     HotSpot3D - 3D mutation proximity analysis program.
-        Version:     V0.6.4
+        Version:     V0.6.5
          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 = 'V0.6.4';
+our $VERSION = 'V0.6.5';
 
 use Carp;
 use FileHandle;

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 = 0.6.4
+version = 0.6.5
 license = Perl_5
 copyright_holder = McDonnell Genome Institute at Washington University
 copyright_year   = 2013

dist.ini

@@ -24,6 +24,8 @@ use FileHandle;
 
 use Data::Dumper;
 
+use TGI::Mutpro::Main::Density;
+
 my $WEIGHT = "weight";
 my $RECURRENCE = "recurrence";
 my $UNIQUE = "unique";
@@ -774,7 +776,8 @@ Usage: hotspot3d cluster [options]
 --3d-distance-cutoff         3D distance cutoff (<), default: 100 (if p-value-cutoff also not set)
 --linear-cutoff              Linear distance cutoff (> peptides), default: 0
 --max-radius                 Maximum cluster radius (max network geodesic from centroid, <= Angstroms), default: 10
---vertex-type                Graph vertex type (recurrence, unique, or weight), default: recurrence
+--clustering                 Cluster using network or density-based methods (network or density), default: network
+--vertex-type                Graph vertex type for network-based clustering (recurrence, unique, or weight), default: recurrence
 --distance-measure           Pair distance to use (closest or average), default: average
 --maf-file                   .maf file used in proximity search step (used if vertex-type = recurrence)
 --transcript-id-header       .maf file column header for transcript id's, default: transcript_name