ms-quant 0.0.3 → 0.0.4

data/VERSION

@@ -1 +1 @@
-0.0.3
+0.0.4

data/bin/peptide_hit_qvalues_to_spectral_counts_table.rb

@@ -165,8 +165,6 @@ protein_groups.each do |protein_group|
   protein_group.peptide_hits.each {|hit| pephit_to_protein_groups[hit] << protein_group }
 end
 
-# partition them all out by filename
-
 counts_parallel_to_names_with_counts_per_group = samplenames.map do |name|
   pep_hit_to_prot_groups = Hash.new {|h,k| h[k] = [] }
   groups_of_pephits = protein_groups.map do |prot_group|
@@ -175,9 +173,9 @@ counts_parallel_to_names_with_counts_per_group = samplenames.map do |name|
       pep_hit_to_prot_groups[pep_hit] << prot_group
     end # returns the group of pep_hits
   end
-  counts = Ms::Quant::SpectralCounts.counts(groups_of_pephits) # do |pephit|
-  #  pephit_to_protein_groups[pephit].size
-  #end
+  counts = Ms::Quant::SpectralCounts.counts(groups_of_pephits) do |pephit|
+    pephit_to_protein_groups[pephit].size
+  end
 end
 
 if opt[:qspec] || opt[:descriptions]
@@ -222,10 +220,17 @@ end
 header_cats.push( *%w(BestID AllIDs) )
 header_cats.push( 'Description' ) if opt[:descriptions]
 
+sort_protein_id = 
+  if id_to_length
+    lambda {|prot_id| [prot_id, -id_to_length[prot_id]] }
+  else
+    lambda {|prot_id| prot_id }
+  end
+
 protein_groups.zip(ar_of_rows) do |zipped|
   (pg, row) = zipped
   # swiss-prot and then the shortest
-  best_protid = pg.sort_by {|prot_id| [prot_id, -id_to_length[prot_id]] }.first
+  best_protid = pg.sort_by(&sort_protein_id).first
   (gene_id, desc) = 
     if opt[:descriptions] 
       desc = id_to_desc[best_protid] 
@@ -238,8 +243,6 @@ protein_groups.zip(ar_of_rows) do |zipped|
   row.push(desc) if desc
 end
 
-### SORT???
-
 File.open(opt[:outfile],'w') do |out|
   out.puts header_cats.join(delimiter) 
   ar_of_rows.each {|row| out.puts row.join(delimiter) }

data/lib/ms/quant/qspec.rb

@@ -28,11 +28,11 @@ class Ms::Quant::Qspec
   def self.results_array(resultsfile)
     rows = IO.readlines(resultsfile).map {|line| line.chomp.split("\t") }
     headers = rows.shift
+    start_bayes = headers.index {|v| v =~ /BayesFactor/i }
     rows.map do |row| 
       data = [row[0]]
-      data.push( *row[1,2].map(&:to_i) )
-      data.push( *row[3,4].map(&:to_f) )
-      data.push( row[7] )
+      data.push( *row[start_bayes,4].map(&:to_f) )
+      data.push( row[start_bayes+4] )
       Results.new(*data)
     end
   end
@@ -74,18 +74,19 @@ class Ms::Quant::Qspec
     write(tfile.path)
     qspec_exe = self.class.executable(conditions)
     cmd = [qspec_exe, tfile.path, NBURNIN, NITER, (normalize ? 1 : 0)].join(' ')
-    puts "running #{cmd}" if $VERBOSE
+    if $VERBOSE
+      puts "running #{cmd}" if $VERBOSE
+    else
+      cmd << " 2>&1"
+    end
     reply = `#{cmd}`
     puts reply if $VERBOSE
-    results = self.class.results_array(tfile.path + Results::EXT)
+    results = self.class.results_array(tfile.path + '_' + qspec_exe)
     tfile.unlink
     results
   end
 
   # for version 2 of QSpec
-  Results = Struct.new(:protid, :set0, :set1, :bayes_factor, :fold_change, :rb_stat, :fdr, :flag)
-  class Results
-    EXT = '_qspec'
-  end
+  Results = Struct.new(:protid, :bayes_factor, :fold_change, :rb_stat, :fdr, :flag)
 end
 

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 0
-  - 3
-  version: 0.0.3
+  - 4
+  version: 0.0.4
 platform: ruby
 authors: 
 - John T. Prince
@@ -14,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-03-31 00:00:00 -06:00
+date: 2011-04-04 00:00:00 -06:00
 default_executable: peptide_hit_qvalues_to_spectral_counts_table.rb
 dependencies: 
 - !ruby/object:Gem::Dependency