RubyGems - mspire - Versions diffs - 0.1.5 → 0.1.7 - Mend

mspire 0.1.5 → 0.1.7

Files changed (47) hide show

data/Rakefile +5 -2
data/bin/bioworks_to_pepxml.rb +84 -40
data/bin/fasta_shaker.rb +100 -0
data/bin/filter_spec_id.rb +185 -23
data/bin/gi2annot.rb +2 -110
data/bin/id_class_anal.rb +31 -21
data/bin/id_precision.rb +12 -8
data/bin/{false_positive_rate.rb → precision.rb} +1 -1
data/bin/protein_summary.rb +55 -62
data/changelog.txt +34 -0
data/lib/align.rb +0 -1
data/lib/fasta.rb +88 -24
data/lib/gi.rb +114 -0
data/lib/roc.rb +64 -58
data/lib/spec_id/aa_freqs.rb +166 -0
data/lib/spec_id/bioworks.rb +5 -1
data/lib/spec_id/precision.rb +427 -0
data/lib/spec_id/proph.rb +2 -2
data/lib/spec_id/sequest.rb +810 -113
data/lib/spec_id/srf.rb +486 -0
data/lib/spec_id.rb +107 -23
data/release_notes.txt +11 -0
data/script/estimate_fpr_by_cysteine.rb +226 -0
data/script/filter-peps.rb +3 -3
data/script/find_cysteine_background.rb +137 -0
data/script/gen_database_searching.rb +11 -7
data/script/genuine_tps_and_probs.rb +136 -0
data/script/top_hit_per_scan.rb +5 -2
data/test/tc_aa_freqs.rb +59 -0
data/test/tc_bioworks.rb +6 -1
data/test/tc_bioworks_to_pepxml.rb +25 -18
data/test/tc_fasta.rb +81 -3
data/test/tc_fasta_shaker.rb +147 -0
data/test/tc_gi.rb +20 -0
data/test/tc_id_class_anal.rb +9 -12
data/test/tc_id_precision.rb +12 -11
data/test/{tc_false_positive_rate.rb → tc_precision.rb} +13 -22
data/test/tc_protein_summary.rb +31 -22
data/test/tc_roc.rb +95 -50
data/test/tc_sequest.rb +212 -145
data/test/tc_spec.rb +10 -5
data/test/tc_spec_id.rb +0 -2
data/test/tc_spec_id_xml.rb +36 -0
data/test/tc_srf.rb +216 -0
metadata +35 -21
data/lib/spec_id/false_positive_rate.rb +0 -476
data/test/tc_gi2annot.rb +0 -12

data/lib/spec_id/false_positive_rate.rb DELETED Viewed

@@ -1,476 +0,0 @@
-# for false_positive_rate:
-require 'optparse'
-require 'ostruct'
-require 'generator'
-require 'gnuplot'
-require 'roc'
-class String
-  def margin
-    self.gsub(/^\s*\|/,'')
-  end
-end
-class SpecID
-  class FalsePositiveRate
-    module HTML
-      # html and body tags
-      def html
-        "|<html>
-         |#{yield}
-         |</html>\n".margin
-      end
-      def body
-        "|<body>
-         |  #{yield}
-         |</body>\n".margin
-      end
-      def header
-        "|<head>
-         |  #{style}
-         |</head>\n".margin
-      end
-      def td
-        "<td>#{yield}</td>"
-      end
-      def style
-        '
-     <style type="text/css">
-        div#tp_table {
-          text-align: center;
-          margin-top: 50px;
-          margin-bottom: 50px;
-        }
-        span.code {
-        font-family: Courier,Monospace;
-        font-size: 80%;
-        }
-          table {
-              border-width:1px;
-              border-color:#CCCCCC;
-              border-collapse: collapse;
-          }
-          caption {
-            font-size: 90%;
-          }
-          td,th {
-              padding-top: 2px;
-              padding-bottom: 2px;
-              padding-left: 1;
-              padding-right: 1;
-          }
-          th.small {
-            font-size: 80%;
-            font-weight: normal;
-            padding: 1px;
-          }
-          td.redline {
-              background-color: #FF0000;
-              color: #FFFFFF
-          }
-      div#plot {
-        margin: 30px;
-     text-align:center
-      }
-      hr {color: sienna}
-      body { font-size: 8pt; font-family: Arial,Helvetica,Times}
-      </style>
-        '
-      end
-      def table
-        "|<table border=\"1\" align=\"center\" style=\"font-size:100%\">
-         |  #{yield}
-         |</table>\n".margin
-      end
-      def tr
-        "|<tr>
-         |  #{yield}
-         |</tr>\n".margin
-      end
-    end # module HTML
-  end # class FalsePositiveRate
-end #class SpecID
-class SpecID
-  class FalsePositiveRate
-    ###########################################################
-    # GLOBAL SETTINGS:
-    DEF_PREFIX = "INV_"
-    DATA_PREC = 4   # decimal places of precision or fpr data
-    STDOUT_JTPLOT_BASE = "fpr"  # if there is no outfile
-    ###########################################################
-    include SpecID::FalsePositiveRate::HTML
-    ## returns either an ascii string (if file_as_decoy) or
-    ## returns an html string
-    def false_positive_rate(argv)
-      opt = parse_args(argv)
-      files = argv.to_a
-      file_as_decoy = false
-      if File.exist? opt.f
-        file_as_decoy = true
-        out_string = file_as_decoy(files, opt)
-      else
-        out_string = prefix_as_decoy(files, opt)
-      end
-      return [out_string, opt, file_as_decoy]
-    end
-    def run_cmd_line(argv)
-      output_string, opt, file_as_decoy = false_positive_rate(argv)
-      if file_as_decoy
-        puts output_string
-      else
-        ## open file and write to it..
-        if opt.o == 'STDOUT'
-          print output_string
-        else
-          File.open(opt.o,'w') do |fh| fh.print output_string end
-        end
-      end
-    end
-    # returns the outfile with no extension
-    def outfile_noext(opt)
-      if opt == 'STDOUT'
-      "#{STDOUT_JTPLOT_BASE}"
-      else
-        opt.sub(/#{Regexp.escape(File.extname(opt))}$/, '')
-      end
-    end
-    def file_noext(file)
-      file.sub(/#{Regexp.escape(File.extname(file))}$/, '')
-    end
-    def parse_args(argv)
-      opt = OpenStruct.new
-      opt.f = DEF_PREFIX
-      opt.o = 'STDOUT'
-      opts = OptionParser.new do |op|
-        op.banner = "Usage: #{File.basename(__FILE__)} [options] bioworks.xml|proph-prot.xml ..."
-        op.separator ""
-        op.separator "Abbreviations and Definitions:"
-        op.separator "  TP = True Positives"
-        op.separator "  FP = False Positive"
-        op.separator "  FPR = False Positive Rate = [FP/(TP+FP)] (between 0 and 1)"
-        op.separator "  FPR2 = Gygi's estimation of FPR = [2*FPR]"
-        op.separator "  Precision = [TP/(TP+FP)]"
-        op.separator ""
-        op.separator "Output: "
-        op.separator "  1. Decoy as separate search: FPR to STDOUT"
-        op.separator "  2. Decoy proteins from concatenated database: 'fpr.html'"
-        op.separator ""
-        op.separator "Options:"
-        op.on("-f", "--fp_data <prefix_or_file>", "PREFIX (def: #{DEF_PREFIX}) -or- decoy FILE") {|v| opt.f = v }
-        op.separator ""
-        op.separator "        If searched with a concatenated DB, give a PREFIX to decoy proteins."
-        op.separator "        If files have different prefixes, separate with commas."
-        op.separator "        If searched with a separate decoy DB, give the FILE name of decoy data"
-        op.separator ""
-        op.on("-g", "--gygi", "also show Gygi's estimate of FPR (2*FPR)") {|v| opt.g = v}
-        ## NOT YET FUNCTIONAL: op.on("-e", "--peptides", "do peptides instead of proteins")
-        op.on("-p", "--prec", "also show precision (TP/(TP+FP))") {|v| opt.p = v}
-        op.on("-n", "--nofpr", "don't show FPR") {|v| opt.n = v}
-        op.separator ""
-        op.on("-o", "--outfile <file>", "write output to file (def: #{opt.o})") {|v| opt.o = v}
-        op.on("-a", "--area", "output area under the curve instead of the plot") {|v| opt.a = v}
-        op.on_tail("
-Examples:
-  1. For a search on a concatenated database where the decoy proteins have
-  been flagged with the prefix 'INV_' for both Bioworks and ProteinProphet
-  output:
-    #{File.basename(__FILE__)} -f INV_ bioworks.xml proph-prot.xml
-  2. To determine the false positive rate of a search (and fpr2 and precision)
-  using a normal and decoy database search, filter both the normal and decoy
-  datasets identically, export to xml and run like this (only works for
-  Bioworks xml export):
-    #{File.basename(__FILE__)} -tp -f decoy_bioworks.xml bioworks.xml
-  ")
-      end
-      opts.parse!(argv)
-      if argv.size < 1
-        puts opts
-        exit
-      end
-      opt
-    end
-    # takes a comma separated list and extends the last to create an array of
-    # desired size
-    def prefixes(arg, desired_size)
-      arg_arr = arg.split(',')
-      new_arr = []
-      last_arg = arg_arr[0]
-      desired_size.times do |i|
-        if arg_arr[i]
-          new_arr[i] = arg_arr[i]
-          last_arg = new_arr[i]
-        else
-          new_arr[i] = last_arg
-        end
-      end
-      new_arr
-    end
-    ## collapses arrays to one level deep so we can sync them up
-    def arrays_to_one_level_deep(all_arrs)
-      mostly_flat = []
-      all_arrs.each do |per_file|
-        per_file.each do |per_style|
-          mostly_flat << per_style[0]
-          mostly_flat << per_style[1]
-        end
-      end
-      mostly_flat
-    end
-    # prints rows and th for the data
-    def table_cells(all_arrs, key)
-      ## columns specific headings:
-      all_string = ""
-      all_string << tr do
-        line = ""
-        key.each do |per_file|
-          per_file.each do |per_ds|
-            line << "<th class=\"small\">#{per_ds[1][0]}</th><th class=\"small\">#{per_ds[1][1]}</th>"
-          end
-        end
-        line
-      end
-      mostly_flat = arrays_to_one_level_deep(all_arrs)
-      SyncEnumerator.new(*mostly_flat).each do |row|
-        all_string << tr do
-          string = row.map {|it|
-            sty="%d"
-            if it.class == Float ; sty="%.#{DATA_PREC}f" end
-            td{ sprintf(sty,it)}
-          }.join
-        end
-      end
-      all_string
-    end
-    def html_table_output(all_arrs, key, files, filename_noext)
-      num_datasets_per_file = all_arrs.first.size
-      num_cols_per_dataset = 2
-      big_colspan = num_datasets_per_file * num_cols_per_dataset
-      output = table do
-        tr do
-          files.map do |file|
-        "<th colspan=\"#{big_colspan}\">#{file}</th>"
-          end.join
-        end +
-          tr do
-          key.map do |arr|
-            arr.map do |ds|
-        "<th colspan=\"2\">#{ds.first}</th>"
-            end
-          end
-          end +
-            table_cells(all_arrs, key)
-      end
-    "<div id=\"tp_table\">" + output + "</div>"
-    end
-    def y_axis_label(key)
-      ## We only take the keys for the first file, as it's assumed that the major
-      ## labels will be identical for all of them
-      labels = key.first.map {|tp| tp.first }
-      labels.join "  |  "
-    end
-    # escapes any ' chars
-    def escape_to_gnuplot(string)
-      # long way, but it works.
-      new_string = ""
-      string.split(//).each do |chr|
-        if chr == "'" ; new_string << "\\" end
-        new_string << chr
-      end
-      new_string
-    end
-    ## outputs a .toplot file based on filename_noext, creates a png file, and
-    ## writes  html to fh that will load the png file up
-    ## This is a self contained module that can be swapped out for a
-    ## completely different plotting program if desired.
-    def plot_figure(all_arrs, key, files, filename_noext)
-      ## CREATE the PLOT IMAGE:
-      to_plot = filename_noext+'.toplot'
-      png = filename_noext+'.png'
-      Gnuplot.open do |gp|
-        Gnuplot::Plot.new( gp ) do |plot|
-          plot.terminal "png noenhanced"
-          plot.output png
-          plot.title "Classification Analysis"
-          plot.xlabel 'Num True Positives'
-          plot.ylabel escape_to_gnuplot(y_axis_label(key))
-          plot.style "line 1 lt 1"
-          plot.style "line 2 lt 12"
-          #plot.style  "line 1 lt 1 lw #{opts.lw} pt 7 ps #{opts.ps}",
-          plot.yrange "[-0.05:#{1.0 + 0.2*files.size}]"
-          files.each_with_index do |file,i|
-            key[i].each_with_index do |k,j|
-              plot.data << Gnuplot::DataSet.new( [ all_arrs[i][j][0], all_arrs[i][j][1] ] ) do |ds|
-              ds.with = "lines"
-              ds.title = escape_to_gnuplot("#{file}: #{k[1][1]}")
-            end
-          end
-        end
-      end
-    end
-=begin
-      ## CREATE the PLOT IMAGE:
-      to_plot = filename_noext+'.toplot'
-      png = filename_noext+'.png'
-      File.open(to_plot,'w') do |out|
-        out.puts 'XYData'
-        out.puts filename_noext
-        out.puts "Classification Analysis"
-        out.puts 'Num True Positives'
-        out.puts escape_to_gnuplot(y_axis_label(key))
-        files.each_with_index do |file,i|
-          #p key[i]
-          #p all_arrs[i]
-          key[i].each_with_index do |k,j|
-            out.puts(escape_to_gnuplot("#{file}: #{k[1][1]}"))
-            out.puts all_arrs[i][j][0].join(' ')
-            out.puts all_arrs[i][j][1].join(' ')
-          end
-        end
-      end
-      num_files = files.size
-      if $".include? 'plotter.rb'
-        cmd = "#{to_plot} --yrange n0.05:#{1.0 + 0.2*num_files} --noenhanced -w l"
-        plot_cmd = "plot.rb #{cmd}"
-        Plotter.new.plot_string "#{to_plot} --yrange n0.05:#{1.0 + 0.2*num_files} --noenhanced -w l"
-        unless File.file? png
-          abort "Fatal Error in plotting cmd=\"#{plot_cmd}\":\n#{reply}"
-        end
-      else
-        warn "plotter.rb not found, not png plot image available"
-      end
-=end
-      ## CREATE the HTML to load the plot:
-      basename_filename_noext = File.basename(filename_noext)
-      output = "<div id=\"plot\"><table class=\"image\" align=\"center\">\n"
-      #output << "<caption align=\"bottom\">Additional views of this data may be obtained by using the <span class=\"code\">plot.rb</span> command on '#{to_plot}' (type <span class=\"code\">plot.rb</span> for more details). Plot generated with command: &nbsp;&nbsp; <span class=\"code\">#{plot_cmd}</span></caption>\n"
-      output << "<tr><td><img src=\"#{basename_filename_noext}.png\" title=\"File #{basename_filename_noext} must be in the same directory as this html.\"/></td></tr>\n"
-      output << "</table></div>\n"
-      output
-    end  # plot_figure
-    def file_as_decoy(files, opt)
-      bio = SpecID::Bioworks.new
-      puts "Calculating false positive rates using '#{opt.f}' as decoy ..."
-      fps = bio.num_prots(opt.f)
-      out = ""
-      files.each do |file|
-        tps = bio.num_prots(file)
-        out << "*****************************************************\n"
-        out << sprintf("%-36s  # TP : #{tps}\n", file)
-        out << sprintf("%-36s  # FP : #{fps}\n", opt.f)
-        out << sprintf("        False Positive Rate   [FP/(TP+FP)] : %.3f\n", fps.to_f/(tps+fps)) unless opt.n
-        out << sprintf(" Gygi's False Positive Rate 2*[FP/(TP+FP)] : %.3f\n", 2.0*fps/(tps+fps)) if opt.g
-        out << sprintf("                    Precision [TP/(TP+FP)] : %.3f\n", tps.to_f/(tps+fps)) if opt.p
-        out << "*****************************************************\n"
-      end
-      out
-    end
-    def prefix_as_decoy(files, opt)
-      #puts "Calculating false positive rates using prefix #{opt.f} ..."
-      prefix_arr = prefixes(opt.f, files.size)
-      all_arrs = []
-      key = []
-      out_noext = outfile_noext(opt.o)
-      files.each_with_index do |file,i|
-        all_arrs[i] = []
-        key[i] = []
-        sp = SpecID.new(file)
-        #headers = ["#{file_noext(file)} Precision [TP/(TP+FP)]", "#{file_noext(file)} FPR [FP/(FP+TP)]"]
-        (tp, prec, fpr2) = sp.tps_and_precision_and_fpr2_times2_for_prob(prefix_arr[i])
-        if opt.g
-          all_arrs[i] << [tp,fpr2]
-          key[i] <<  ["Gygi FPR", ["#TP", "Gygi FPR = 2*FP/(TP+FP)"]]
-        end
-        if opt.p
-          all_arrs[i] << [tp,prec]
-          key[i] <<  ["Prec", ["#TP", "Prec = TP/(TP+FP)"]]
-        end
-        unless opt.n
-          ## Add the fpr datasets
-          fpr = fpr2.map {|v| v/2.0}
-          all_arrs[i] << [tp,fpr]
-          key[i] <<  ["FPR", ["#TP", "FPR = FP/(TP+FP)"]]
-        end
-      end
-      string = ''
-      if opt.a
-        roc = ROC.new
-        #string << "***********************************************************\n"
-        #string << "AREA UNDER CURVE:\n"
-        key.each_with_index do |file,i|
-          string << "#{files[i]} (area under curve)\n"
-          key[i].each_index do |j|
-            string << "#{key[i][j][0]} [#{ key[i][j][1]}]:\t"
-            tps = all_arrs[i][j][0]
-            oth = all_arrs[i][j][1]
-            string << roc.area_under_curve(tps, oth).to_s << "\n"
-          end
-        end
-        #string << "***********************************************************\n"
-      else
-        string = html do
-          header +
-            body do
-            plot_figure(all_arrs, key, files, out_noext) +
-              html_table_output(all_arrs, key, files, out_noext)
-            end
-        end
-      end
-      string
-    end
-  end # class FalsePositiveRate
-end # class SpecID

data/test/tc_gi2annot.rb DELETED Viewed

@@ -1,12 +0,0 @@
-require 'test/unit'
-class Gi2AnnotTest < Test::Unit::TestCase
-  ROOT_DIR = File.join(File.dirname(__FILE__), '..')
-  def test_query
-    # @TODO: Add in some kind of skip if there is no internet connection
-    assert_equal('CP4-57 prophage; RNase LS [Escherichia coli K12]'+"\n", `ruby -I#{File.join(ROOT_DIR, 'lib')} #{File.join(ROOT_DIR, 'bin', 'gi2annot.rb')} 16130548`)
-  end
-end