ms-quant 0.0.6 → 0.1.0

data/VERSION

@@ -1 +1 @@
-0.0.6
+0.1.0

data/bin/peptide_hit_qvalues_to_spectral_counts_table.rb

@@ -92,6 +92,7 @@ psq is really .psq.tsv file
   opt :verbose, "speak up", :default => false
   opt :count_type, "type of spectral counts (<spectral|aaseqcharge|aaseq>)", :default => 'spectral'
   opt :qspec_normalize, "normalize spectral counts per run", :default => false
+  opt :qspec_keep_files, "keep a copy of the files submitted and returned from Qspec", :default => false
   opt :write_subset, "(dev use only) write subset db", :default => false
 end
 
@@ -201,13 +202,15 @@ counts_table = Ruport::Data::Table.new(:data => counts_data, :column_names => sa
 if opt[:qspec]
 
   # prepare data for qspec
-  condition_to_count_array = counts_table.column_names.map {|name| [name, counts_table.column(name)] }
+  condition_to_count_array = counts_table.column_names.map do |name| 
+    [samplename_to_condition[name], counts_table.column(name)] 
+  end
   # average length of the proteins in the group
   name_length_pairs = protein_groups.map do |pg|
-    [pg.join(":"), pg.map(&:length).reduce(:+)./(pg.size).round]
+    [pg.map(&:id).join(":"), pg.map(&:length).reduce(:+)./(pg.size).round]
   end
 
-  qspec_results = Ms::Quant::Qspec.new(name_length_pairs, condition_to_count_array).run(opt[:qspec_normalize])
+  qspec_results = Ms::Quant::Qspec.new(name_length_pairs, condition_to_count_array).run(opt[:qspec_normalize], :keep => opt[:qspec_keep_files])
   
   cols_to_add = [:bayes_factor, :fold_change, :fdr]
   counts_table.add_columns cols_to_add

data/lib/ms/quant/qspec.rb

@@ -8,6 +8,8 @@ class Ms::Quant::Qspec
   INIT_HEADER = %w(protid protLen)
   DELIMITER = "\t"
 
+  SUBMITTED_TO_QSPEC = 'submitted_to_qspec.txt'
+
   # takes an ordered list of conditions ['cond1', 'cond1', 'cond2', 'cond2'] and
   # returns an array of ints [0,0,0,1,1,1...]
   def self.conditions_to_ints(conditions)
@@ -75,6 +77,11 @@ class Ms::Quant::Qspec
     puts "normalize: #{normalize}" if $VERBOSE
     tfile = Tempfile.new("qspec")
     write(tfile.path)
+    if opts[:keep]
+      local_file = File.join(Dir.pwd,File.basename(tfile.path))
+      FileUtils.cp(tfile.path, local_file, :verbose => $VERBOSE)
+      puts "(copy of) file submitted to qspec: #{local_file}" if $VERBOSE
+    end
     qspec_exe = self.class.executable(conditions)
     cmd = [qspec_exe, tfile.path, NBURNIN, NITER, (normalize ? 1 : 0)].join(' ')
     if $VERBOSE
@@ -84,7 +91,13 @@ class Ms::Quant::Qspec
     end
     reply = `#{cmd}`
     puts reply if $VERBOSE
-    results = self.class.results_array(tfile.path + '_' + qspec_exe)
+    outfile = tfile.path + '_' + qspec_exe
+    results = self.class.results_array(outfile)
+    if opts[:keep]
+      local_outfile = File.join(Dir.pwd, File.basename(outfile))
+      FileUtils.cp(outfile, local_outfile, :verbose => $VERBOSE)
+      puts "(copy of) file returned from qspec: #{outfile}"
+    end
     tfile.unlink
     results
   end

data/lib/ms/quant/spectral_counts.rb

@@ -5,6 +5,13 @@ module Ms
   module Quant
     module SpectralCounts
       Counts = Struct.new(:spectral, :aaseqcharge, :aaseq)
+      class Counts
+        def initialize(*args)
+          super(*args)
+          # default is zero counts
+          self[0] ||= 0.0 ; self[1] ||= 0.0 ; self[2] ||= 0.0
+        end
+      end
 
       # returns a parallel array of Count objects.  If split_hits then counts
       # are split between groups sharing the hit.  peptide_hits must respond

metadata

@@ -2,7 +2,7 @@
 name: ms-quant
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.0.6
+  version: 0.1.0
 platform: ruby
 authors: 
 - John T. Prince
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-04-26 00:00:00 -06:00
+date: 2011-05-05 00:00:00 -06:00
 default_executable: peptide_hit_qvalues_to_spectral_counts_table.rb
 dependencies: 
 - !ruby/object:Gem::Dependency