mspire 0.2.2 → 0.2.4

data/Rakefile

@@ -140,7 +140,7 @@ tm = Time.now
 spec = Gem::Specification.new do |s|
   s.platform = Gem::Platform::RUBY
   s.name = NAME
-  s.version = "0.2.2"
+  s.version = "0.2.4"
   s.summary = "Mass Spectrometry Proteomics Objects, Scripts, and Executables"
   s.date = "#{tm.year}-#{tm.month}-#{tm.day}"
   s.email = "jprince@icmb.utexas.edu"

data/bin/bioworks_to_pepxml_gui.rb

@@ -0,0 +1,225 @@
+#!/usr/bin/ruby -w
+
+tmp = $VERBOSE ; $VERBOSE = nil
+require 'fox16'
+$VERBOSE = tmp
+
+include Fox
+
+
+class Opt
+  attr_accessor :flag, :value
+  def initialize(flag, value=nil)
+    @flag = flag
+    @value = value
+  end
+
+  def self.[](flag, value=nil)
+    self.new(flag, value)
+  end
+
+  def to_s
+    st = @flag
+    if @value
+      st << " " << @value
+    end
+    st
+  end
+  
+end
+
+
+NCOLS = 40
+
+srf_dir = nil
+output_dir = '.'
+msdata_dir = '.'
+$progname = 'bioworks_to_pepxml.rb'
+$sequest_folder = '/project/marcotte/marcotte/ms/john/sequest'
+$data_folder = '/project/marcotte/marcotte/ms/john/data'
+$isb_folder = '/var/www/tpp'
+
+# This is a directory selector consisting of: Label | FieldText | BrowseButton
+# if you pass in patterns, then you can select multiple files!
+class DirSelector 
+  attr_writer :directory
+
+  def directory
+    @directory_data.to_s
+  end
+
+  # You should pass in the frame that you want filled up!
+  def initialize(parent, label='select directory', init_dir='.', text_field_width=30)
+    @directory_data = FXDataTarget.new(init_dir)
+
+    FXLabel.new(parent, label , nil, LAYOUT_CENTER_Y|LAYOUT_RIGHT|JUSTIFY_RIGHT)
+    srf_field = FXTextField.new(parent, text_field_width, @directory_data) do |tf|
+      tf.text = @directory_data.to_s
+    end
+    srf_field.connect(SEL_COMMAND) do |sender, sel, message|
+      @directory_data.value = message
+    end
+    but = FXButton.new(parent, "Browse")
+    but.connect(SEL_COMMAND) do |sender, sel, message|
+      @directory_data.value = FXFileDialog.getOpenDirectory(parent, "Open directory_data", @directory_data.to_s)
+      srf_field.text = @directory_data.value
+    end
+  end
+end
+
+# This is a directory selector consisting of: Label | FieldText | BrowseButton
+# if you pass in patterns, then you can select multiple files!
+class MultipleFilesSelector
+  # an array of filenames
+  attr_writer :files
+
+  # You should pass in the frame that you want filled up!
+  def initialize(parent, label='select multiple files', init_dir='.', text_field_width=30, patterns=["All Files (*)"])
+    @directory_data = FXDataTarget.new(init_dir)
+
+    FXLabel.new(parent, label , nil, LAYOUT_CENTER_Y|LAYOUT_RIGHT|JUSTIFY_RIGHT)
+    srf_field = FXTextField.new(parent, text_field_width, @directory_data) do |tf|
+      tf.text = @directory_data.to_s
+    end
+    srf_field.connect(SEL_COMMAND) do |sender, sel, message|
+      @directory_data.value = message
+    end
+    but = FXButton.new(parent, "Browse")
+    if patterns.is_a?(Array)
+      pattern_string = patterns.join("\n") 
+    else
+      pattern_string = patterns
+    end
+    but.connect(SEL_COMMAND) do |sender, sel, message|
+      reply = FXFileDialog.getOpenFilenames(parent, "Open directory_data", @directory_data.to_s, pattern_string)
+      p reply
+      abort
+      srf_field.text = @directory_data.value
+    end
+  end
+end
+
+
+class MainWindow < FXMainWindow
+
+  def action(*args)
+    p args
+
+    cmd = []
+    cmd << $progname
+    #cmd << args
+    #cmd << Opt['-o', output_dir]
+
+    puts cmd.join(" ")
+  end
+
+  def initialize(anApp)
+    labels = ["&SRF files (select multiple)", "&Output Directory (ISB)", "&Directory with RAW files"]
+    super(anApp, "bioworks_to_pepxml", nil, nil, DECOR_ALL)
+
+    gb = FXGroupBox.new(self, "Specify input/output", FRAME_RIDGE)
+    mat = FXMatrix.new(gb, 3, MATRIX_BY_COLUMNS|LAYOUT_SIDE_TOP)
+
+    srf_files_selector = MultipleFilesSelector.new(mat, labels[0], $sequest_folder, NCOLS, ["SRF files (*.srf)"])
+
+    isb_files_selector = DirSelector.new(mat, labels[1], $isb_folder, NCOLS)
+
+    hf = FXHorizontalFrame.new(self)
+    create_mzxml = FXCheckButton.new(hf, 'create mzXML files')
+    copy_mzxml = FXCheckButton.new(hf, 'copy mzXML files to ISB dir') {|v| v.checkState = TRUE }
+    copy_mzxml.hide
+
+    @mat2 = FXMatrix.new(self, 3, MATRIX_BY_COLUMNS|LAYOUT_SIDE_TOP)
+    srf_dir_selector = DirSelector.new(@mat2, labels[2], $data_folder, NCOLS)
+
+    submit = FXButton.new(self, "Submit")
+    submit.connect(SEL_COMMAND) do |sender, sel, message|
+      action(srf_dir_selector.files)
+    end
+
+    create_mzxml.connect(SEL_COMMAND) do |button,b,checked|
+      if checked 
+        copy_mzxml.show
+        @mat2.show
+        self.resize(self.width, @large_height)
+      else
+        copy_mzxml.hide
+        @mat2.hide
+        self.resize(self.width, @small_height)
+      end
+    end
+
+  end
+
+  def create
+    super
+    show(PLACEMENT_SCREEN)
+    @large_height = self.height
+
+    # setup hidden state
+    @mat2.hide 
+    @small_height = @large_height - @mat2.height
+    self.resize(self.width, @small_height)
+  end
+
+end
+
+
+application = FXApp.new("Hello", "FXRuby") do |theApp|
+  MainWindow.new(theApp)
+  theApp.create
+  theApp.run
+end
+
+
+application.run()
+
+
+
+
+=begin
+
+
+---------------------------------
+class MyMainWindow < FXMainWindow
+
+   attr :advancedFrame
+
+   def initialize(app)
+      super(app, "MyMainWindow")
+      
+      contents = FXVerticalFrame.new(self,
+         LAYOUT_FILL_X|LAYOUT_FILL_Y)
+
+      advancedButton = FXButton.new(contents, "Advanced >>",
+         nil, self, 0, FRAME_RAISED|FRAME_THICK)
+
+      advancedButton.connect(SEL_COMMAND) do
+         if @advancedFrame.shown?
+            self.height -= @advancedFrame.height
+            @advancedFrame.hide
+            advancedButton.text = "Advanced >>"
+         else
+            self.height += @advancedFrame.height
+            @advancedFrame.show
+            advancedButton.text = "<< Basic"
+         end
+         
+         self.recalc
+      end
+   end
+end
+#---------------------------
+app = FXApp.new
+
+mainWindow = MyMainWindow.new(app)
+
+app.create
+mainWindow.advancedFrame.hide
+mainWindow.height -= mainWindow.advancedFrame.height
+
+mainWindow.show(PLACEMENT_SCREEN)
+
+app.run
+
+=end

data/changelog.txt

@@ -49,3 +49,8 @@ minor bugfix
 made compatible with Bioworks fasta file reverser and updated tutorial.
 Killed classify_by_prefix routine in favor of classify_by_false_flag which has
 a prefix option
+
+## version 0.2.3
+
+in protein_summary.rb added handling for proteins with no annotation. (either
+dispaly NA or use gi2annnot to grab them from NCBI)

data/lib/gi.rb

@@ -51,7 +51,12 @@ class GI
       #puts url
       begin
         open(url) do |handle|
-          annots.push( *(parse_etool_output(handle)) )
+          if handle.is_a? StringIO 
+            io_input = handle
+          else
+            io_input = handle.read
+          end
+          annots.push( *(parse_etool_output(io_input)) )
         end
       rescue SocketError
         return nil

data/lib/spec_id/protein_summary.rb

@@ -6,6 +6,7 @@ require 'optparse'
 require 'ostruct'
 require 'spec_id'
 require 'spec_id/precision'
+require 'gi'
 
 #############################################################
 # GLOBALS:
@@ -210,13 +211,26 @@ class ProteinSummary
   # returns a string of the table rows
   # false_positive_rate (give as a %) is the cutoff mark
   # returns the number of proteins at the desired_fppr (if given)
-  def table_rows(uniq_prots, prefix, false_positive_rate_percent, num_cols, desired_fppr, actual_percent_fp, peptide_count_filename=nil)
+  def table_rows(uniq_prots, prefix, false_positive_rate_percent, num_cols, desired_fppr, actual_percent_fp, annotations=nil, peptide_count_filename=nil)
     prot_cnt = 0
+    an_cnt = 0
+ 
     uniq_prots.map do |prot| 
       tr do
         prot_cnt += 1
         gi = accession(prot._protein_name)
-        tds([prot_cnt, prot._probability, ref_html(gi, prot._protein_name), prot.annotation.first._protein_description, prot._percent_coverage, peptide_cell(prot_cnt, prot._unique_stripped_peptides.split('+')), prot._total_number_peptides, prot._pct_spectrum_ids])
+
+        if annotations
+          protein_description = annotations[an_cnt]
+          an_cnt += 1
+        else
+          if prot.annotation.size > 0
+            protein_description = prot.annotation.first._protein_description
+          else
+            protein_description = 'NA'
+          end
+        end
+        tds([prot_cnt, prot._probability, ref_html(gi, prot._protein_name), protein_description, prot._percent_coverage, peptide_cell(prot_cnt, prot._unique_stripped_peptides.split('+')), prot._total_number_peptides, prot._pct_spectrum_ids])
       end
     end.join
   end
@@ -310,8 +324,15 @@ class ProteinSummary
 
     output_peptide_counts_file(filtered_sorted_prots, opt.peptide_count) if opt.peptide_count
 
+    # get an array of annotations (or nil if no option)
+    annotations =
+      if opt.get_annotation
+        gis = filtered_sorted_prots.map {|prot| accession(prot._protein_name) }
+        GI.gi2annot(gis) 
+      end
+
     table_string = table do 
-      tr{theaders} + table_rows(filtered_sorted_prots, opt.f, actual_percent_fp, num_cols, opt.c.to_f, actual_percent_fp, opt.peptide_count)
+      tr{theaders} + table_rows(filtered_sorted_prots, opt.f, actual_percent_fp, num_cols, opt.c.to_f, actual_percent_fp, annotations, opt.peptide_count)
     end
     er_info = opt.precision ? error_info(file) : ""
     html_pieces = [outfn, header, fppr_output_as_html, er_info, file_info(file), protproph_script_info, num_prots_html, table_string, trailer]
@@ -410,6 +431,8 @@ class ProteinSummary
       op.separator "Specific to ProteinProphet (with no concatenated DB):"
       op.on("-c", "--cutoff percent", "false positive predictive rate (FPPR)% for given cutoff") {|v| opt.c = v }
       op.on("--cut_at percent", "only reports proteins within FPPR %") {|v| opt.cut_at = v }
+      op.on("--get_annotation", "retrieves annotation by gi code") {|v| opt.get_annotation = v}
+      op.separator "             (use if your proteins have gi's but no annotation) "
     end
 
     opts.parse!(argv)

data/test/tc_gi.rb

@@ -7,9 +7,9 @@ class Gi2AnnotTest < Test::Unit::TestCase
   ROOT_DIR = File.join(File.dirname(__FILE__), '..')
 
   def test_single_query
-    annot = GI.gi2annot([16130548])
+    annot = GI.gi2annot([836805])
     if annot
-      assert_equal('CP4-57 prophage; RNase LS [Escherichia coli K12]', annot.first)
+      assert_equal('proteosome component PRE4 [Saccharomyces cerevisiae]', annot.first)
     else
       assert_nil( puts("SKIPPING gi test (no internet connection available)") )
     end

data/test/tc_spec_id.rb

@@ -126,7 +126,6 @@ class TestOccamsRazor < Test::Unit::TestCase
     prots[1].peps = [peps[2]]  ## should be missing
 
     test_prots = prots[0,2]
-    require 'pp'
     answ = SpecID.occams_razor(test_prots)
     answ.each do |an|
       assert( an[0].is_a?(SpecID::Prot), "prots are there")
@@ -135,6 +134,16 @@ class TestOccamsRazor < Test::Unit::TestCase
     assert_equal( prots[0], first[0])
     assert_equal_array_content( prots[0].peps, first[1])
 
+    require 'pp'
+    #pp answ
+
+
+    prots[0].peps = peps[0,4]
+    prots[1].peps = [peps[2]]  ## should be missing
+    prots[2].peps = []  ## should be missing
+
+    answ = SpecID.occams_razor(test_prots, true)
+    #pp answ
 
 
     #prots[2].peps = [peps[2]]

metadata

@@ -3,8 +3,8 @@ rubygems_version: 0.9.2
 specification_version: 1
 name: mspire
 version: !ruby/object:Gem::Version 
-  version: 0.2.2
-date: 2007-05-08 00:00:00 -05:00
+  version: 0.2.4
+date: 2007-05-17 00:00:00 -05:00
 summary: Mass Spectrometry Proteomics Objects, Scripts, and Executables
 require_paths: 
 - lib
@@ -63,9 +63,9 @@ files:
 - LICENSE
 - changelog.txt
 - release_notes.txt
+- bin/bioworks_to_pepxml_gui.rb
 - bin/gi2annot.rb
 - bin/protein_summary.rb
-- bin/bioworks2sequestXML_gui.rb
 - bin/bioworks2excel.rb
 - bin/pepproph_filter.rb
 - bin/fasta_shaker.rb
@@ -129,9 +129,9 @@ extra_rdoc_files:
 - INSTALL
 - LICENSE
 executables: 
+- bioworks_to_pepxml_gui.rb
 - gi2annot.rb
 - protein_summary.rb
-- bioworks2sequestXML_gui.rb
 - bioworks2excel.rb
 - pepproph_filter.rb
 - fasta_shaker.rb

data/bin/bioworks2sequestXML_gui.rb

@@ -1,67 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'fox14'
-
-include Fox
-
-class DirListWindow < FXMainWindow
-
-  def initialize(app)
-    # Invoke the base class initialize first
-    super(app, "Directory List", nil, nil, DECOR_ALL, 0, 0, 800, 600)
-
-    # Make menu bar
-    menubar = FXMenuBar.new(self, LAYOUT_FILL_X)
-    filemenu = FXMenuPane.new(self)
-    FXMenuCommand.new(filemenu, "&Quit\tCtl-Q", nil, getApp(), FXApp::ID_QUIT)
-    FXMenuTitle.new(menubar, "&File", nil, filemenu)
-    helpmenu = FXMenuPane.new(self)
-    FXMenuCommand.new(helpmenu, "&About FOX...").connect(SEL_COMMAND) {
-      FXMessageBox.information(self, MBOX_OK, "About FOX",
-        "FOX is a really, really cool C++ library...\n" +
-        "and FXRuby is an even cooler GUI for Ruby!")
-    }
-    matrix = FXMatrix.new(menubar, 2, MATRIX_BY_COLUMNS|LAYOUT_FILL_X)
-    FXLabel.new(matrix, "sequest.params:", nil,
-      JUSTIFY_LEFT|LAYOUT_FILL_X|LAYOUT_CENTER_Y)
-    
-    FXMenuTitle.new(menubar, "&Help", nil, helpmenu, LAYOUT_RIGHT)
-
-    # Text field at bottom
-    text = FXTextField.new(self, 10, nil, 0,
-      LAYOUT_SIDE_BOTTOM|LAYOUT_FILL_X|FRAME_SUNKEN|FRAME_THICK)
-  
-    # Make contents
-    dirlist = FXDirList.new(self, nil, 0, (HSCROLLING_OFF|
-      TREELIST_SHOWS_LINES|TREELIST_SHOWS_BOXES|FRAME_SUNKEN|FRAME_THICK|
-      LAYOUT_FILL_X|LAYOUT_FILL_Y), 0, 0, 0, 0)
-  
-    # Now make the directory list widget (dirlist) the message target
-    # for the text field. If you type a new directory name in the text
-    # field the directory list should navigate to that directory.
-    text.target = dirlist
-    text.selector = FXWindow::ID_SETVALUE
-  end
-
-  # Create and show the main window
-  def create
-    super
-    show(PLACEMENT_SCREEN)
-  end
-end
-
-def run
-  # Make application
-  application = FXApp.new("DirList", "FoxTest")
-  
-  # Make window
-  DirListWindow.new(application)
-  
-  # Create app  
-  application.create
-  
-  # Run
-  application.run
-end
-
-run