fixed aliases in bashrc

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1144 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_conf/bashrc b/bp_conf/bashrc
index 17d9c1a293059ef6c40beb81ec31a2ec031bb58d..10e78870f26ce3ca9d4ad15ab2c3620fe6264479 100644 (file)
--- a/bp_conf/bashrc
+++ b/bp_conf/bashrc
@@ -32,6 +32,11 @@ export PERL5LIB="$PERL5LIB:$BP_PERL"
 
 export RUBYLIB="$RUBYLIB:$BP_RUBY/Maasha/lib"
 
+### Some useful aliases.
+
+alias bp_update="cd $BP_DIR && svn update; cd $BP_DIR/bp_usage && svn update;"
+alias bp_test="$BP_DIR/bp_test/test_all"
+
 ### >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 

diff --git a/code_ruby/Maasha/lib/seq.rb b/code_ruby/Maasha/lib/seq.rb
index a7971000ecd11a7d63640e1d21475e8130752141..29132370f97dc84bf66678a29a5eae056010dec6 100644 (file)
--- a/code_ruby/Maasha/lib/seq.rb
+++ b/code_ruby/Maasha/lib/seq.rb
@@ -1,4 +1,5 @@
 require 'patscan'
+require 'patfind'
 
 # Residue alphabets
 DNA     = %w[a t c g]
@@ -14,6 +15,8 @@ SCORE_ILLUMINA = 64
 class SeqError < StandardError; end
 
 class Seq
+  include PatFind
+
   attr_accessor :seq_name, :seq, :type, :qual
 
   # Initialize a sequence object with the following arguments: