lederhosen 0.5.4 → 0.5.5

data/lederhosen.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "0.5.4"
+  s.version = "0.5.5"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]
-  s.date = "2012-08-28"
+  s.date = "2012-09-05"
   s.description = "Various tools for OTU clustering"
   s.email = "harekrishna@gmail.com"
   s.executables = ["lederhosen"]

data/lib/lederhosen/cli.rb

@@ -7,10 +7,20 @@ module Lederhosen
     include Thor::Actions
 
     no_tasks do
+
+      ##
+      # print a status message to $stderr
+      # use for good statuses
+      #
       def ohai(s)
         @shell.say_status('okay', s, 'green')
       end
 
+      ##
+      # print a status message to $stderr
+      # use for bad statuses
+      # also exit's with -1 status-code
+      #
       def ohno(s)
         @shell.say_status('fail', s, 'red')
         exit(-1)

data/lib/lederhosen/tasks/add_names.rb

@@ -49,7 +49,8 @@ module Lederhosen
 
           # Only get first match
           # TODO something smarter here
-          cluster_id = line[0].split(':')[3]
+
+          cluster_id = "cluster-#{line[0].match(/cluster-(\d*)/)[1]}"
           next if clusterid_to_name.include? cluster_id
 
           taxonomic_description = line[1]
@@ -58,7 +59,7 @@ module Lederhosen
           # Example:
           # [0]Bacteria;[1]Actinobacteria;[2]Actinobacteria;[3]Acidimicrobiales;[4]Acidimicrobiaceae;[5]Acidimicrobium;[6]Acidimicrobium_ferrooxidans;
           # I want to match Actinobacteria given level_no = 2
-          level_name = taxonomic_description.match(/\[#{level_no}\](\w*)[;\[]/)[1] rescue next
+          level_name = taxonomic_description.match(/\[#{level_no}\](\w*)[;\[]/)[1] rescue nil
 
           # keep cluster id if name is 'null' (bad taxonomic description)
           # but put paranthesis around it so I know
@@ -68,6 +69,8 @@ module Lederhosen
         end
       end
 
+      ohai "#{clusterid_to_name.keys.size} clusters were identified"
+
       # load table, replace cluster names with taxonomic descriptions
       output = File.open(output, 'w') unless output == $stdout
       ohai "replacing names in #{table}"

data/lib/lederhosen/version.rb

@@ -2,7 +2,7 @@ module Lederhosen
   module Version
     MAJOR = 0
     MINOR = 5
-    PATCH = 4
+    PATCH = 5
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: lederhosen
 version: !ruby/object:Gem::Version 
-  hash: 3
+  hash: 1
   prerelease: 
   segments: 
   - 0
   - 5
-  - 4
-  version: 0.5.4
+  - 5
+  version: 0.5.5
 platform: ruby
 authors: 
 - Austin G. Davis-Richardson
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-08-28 00:00:00 Z
+date: 2012-09-05 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   type: :runtime