added missing files

[biopieces.git] / code_perl / Maasha / Config.pm

diff --git a/code_perl/Maasha/Config.pm b/code_perl/Maasha/Config.pm
index 03bf0ecec195eeb04427439b673db60760818f0d..30e8bb1477daf0aea16e3a3d91b29c391cb959d0 100644 (file)
--- a/code_perl/Maasha/Config.pm
+++ b/code_perl/Maasha/Config.pm
@@ -28,6 +28,7 @@ package Maasha::Config;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Data::Dumper;
 use vars qw( @ISA @EXPORT );
@@ -183,42 +184,6 @@ sub genome_vmatch
 }
 
 
-sub genome_phastcons
-{
-    # Martin A. Hansen, January 2008.
-
-    # Returns the full path to the location of a concatenated
-    # PhastCons file for a given genome.
-
-    my ( $genome,   # requested genome
-       ) = @_;
-
-    # Returns a string.
-    
-    my $file = "$BP_DATA/genomes/$genome/phastcons/$genome.pp";
-
-    return $file;
-}
-
-
-sub genome_phastcons_index
-{
-    # Martin A. Hansen, January 2008.
-
-    # Returns the full path to the location of a PhastCons index
-    # for a given genome.
-
-    my ( $genome,   # requested genome
-       ) = @_;
-
-    # Returns a string.
-    
-    my $file = "$BP_DATA/genomes/$genome/phastcons/$genome.pp.index";
-
-    return $file;
-}
-
-
 sub genomes
 {
     # Martin A. Hansen, February 2008.
@@ -290,42 +255,6 @@ sub chromosomes
 }
 
 
-sub maf_track
-{
-    # Martin A. Hansen, April 2008.
-
-    # Given a genome returns the corresponding mafTrack database table name.
-
-    my ( $genome,   # genome to lookup.
-       ) = @_;
-
-    # Returns a string.
-
-    my ( %hash );
-
-    # The below has should be in a config file - fix later.
-
-    %hash = (
-        danRer4 => 'multiz7way',
-        dm2     => 'multiz15way',
-        dm3     => 'multiz15way',
-        fr2     => 'multiz7way',
-        galGal3 => 'multiz7way',
-        gasAcu1 => 'multiz7way',
-        hg18    => 'multiz17way',
-        mm8     => 'multiz17way',
-        mm9     => 'multiz17way',
-        oryLat1 => 'multiz7way',
-        panTro2 => 'multiz17way',
-        tetNig1 => 'multiz7way',
-    );
-
-    Maasha::Common::error( qw(multiz track not found) ) if not exists $hash{ $genome };
-
-    return $hash{ $genome };
-}
-
-
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 1;