RubyGems - mspire - Versions diffs - 0.2.4 → 0.3.0 - Mend

mspire 0.2.4 → 0.3.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (233) hide show

data/INSTALL +1 -0
data/README +25 -0
data/Rakefile +129 -40
data/bin/{find_aa_freq.rb → aafreqs.rb} +2 -2
data/bin/bioworks_to_pepxml.rb +1 -0
data/bin/fasta_shaker.rb +1 -96
data/bin/filter_and_validate.rb +5 -0
data/bin/{mzxml_to_lmat.rb → ms_to_lmat.rb} +8 -7
data/bin/prob_validate.rb +6 -0
data/bin/raw_to_mzXML.rb +2 -2
data/bin/srf_group.rb +1 -0
data/bin/srf_to_sqt.rb +40 -0
data/changelog.txt +68 -0
data/lib/align/chams.rb +6 -6
data/lib/align.rb +4 -3
data/lib/bsearch.rb +120 -0
data/lib/fasta.rb +318 -86
data/lib/group_by.rb +10 -0
data/lib/index_by.rb +11 -0
data/lib/merge_deep.rb +21 -0
data/lib/{spec → ms/converter}/mzxml.rb +77 -109
data/lib/ms/gradient_program.rb +171 -0
data/lib/ms/msrun.rb +209 -0
data/lib/{spec/msrun.rb → ms/msrun_index.rb} +7 -40
data/lib/ms/parser/mzdata/axml.rb +12 -0
data/lib/ms/parser/mzdata/dom.rb +160 -0
data/lib/ms/parser/mzdata/libxml.rb +7 -0
data/lib/ms/parser/mzdata.rb +25 -0
data/lib/ms/parser/mzxml/axml.rb +11 -0
data/lib/ms/parser/mzxml/dom.rb +159 -0
data/lib/ms/parser/mzxml/hpricot.rb +253 -0
data/lib/ms/parser/mzxml/libxml.rb +15 -0
data/lib/ms/parser/mzxml/regexp.rb +122 -0
data/lib/ms/parser/mzxml/rexml.rb +72 -0
data/lib/ms/parser/mzxml/xmlparser.rb +248 -0
data/lib/ms/parser/mzxml.rb +175 -0
data/lib/ms/parser.rb +108 -0
data/lib/ms/precursor.rb +10 -0
data/lib/ms/scan.rb +81 -0
data/lib/ms/spectrum.rb +193 -0
data/lib/ms.rb +10 -0
data/lib/mspire.rb +4 -0
data/lib/roc.rb +61 -1
data/lib/sample_enzyme.rb +31 -8
data/lib/scan_i.rb +21 -0
data/lib/spec_id/aa_freqs.rb +7 -3
data/lib/spec_id/bioworks.rb +20 -14
data/lib/spec_id/digestor.rb +139 -0
data/lib/spec_id/mass.rb +116 -0
data/lib/spec_id/parser/proph.rb +236 -0
data/lib/spec_id/precision/filter/cmdline.rb +209 -0
data/lib/spec_id/precision/filter/interactive.rb +134 -0
data/lib/spec_id/precision/filter/output.rb +147 -0
data/lib/spec_id/precision/filter.rb +623 -0
data/lib/spec_id/precision/output.rb +60 -0
data/lib/spec_id/precision/prob/cmdline.rb +139 -0
data/lib/spec_id/precision/prob/output.rb +88 -0
data/lib/spec_id/precision/prob.rb +171 -0
data/lib/spec_id/proph/pep_summary.rb +92 -0
data/lib/spec_id/proph/prot_summary.rb +484 -0
data/lib/spec_id/proph.rb +2 -466
data/lib/spec_id/protein_summary.rb +2 -2
data/lib/spec_id/sequest/params.rb +316 -0
data/lib/spec_id/sequest/pepxml.rb +1513 -0
data/lib/spec_id/sequest.rb +2 -1672
data/lib/spec_id/srf.rb +445 -177
data/lib/spec_id.rb +183 -95
data/lib/spec_id_xml.rb +8 -10
data/lib/transmem/phobius.rb +147 -0
data/lib/transmem/toppred.rb +368 -0
data/lib/transmem.rb +157 -0
data/lib/validator/aa.rb +135 -0
data/lib/validator/background.rb +73 -0
data/lib/validator/bias.rb +95 -0
data/lib/validator/cmdline.rb +260 -0
data/lib/validator/decoy.rb +94 -0
data/lib/validator/digestion_based.rb +69 -0
data/lib/validator/probability.rb +48 -0
data/lib/validator/prot_from_pep.rb +234 -0
data/lib/validator/transmem.rb +272 -0
data/lib/validator/true_pos.rb +46 -0
data/lib/validator.rb +214 -0
data/lib/xml.rb +38 -0
data/lib/xml_style_parser.rb +105 -0
data/lib/xmlparser_wrapper.rb +19 -0
data/script/compile_and_plot_smriti_final.rb +97 -0
data/script/extract_gradient_programs.rb +56 -0
data/script/get_apex_values_rexml.rb +44 -0
data/script/mzXML2timeIndex.rb +1 -1
data/script/smriti_final_analysis.rb +103 -0
data/script/toppred_to_yaml.rb +47 -0
data/script/tpp_installer.rb +1 -1
data/{test/tc_align.rb → specs/align_spec.rb} +21 -27
data/{test/tc_bioworks_to_pepxml.rb → specs/bin/bioworks_to_pepxml_spec.rb} +25 -41
data/specs/bin/fasta_shaker_spec.rb +259 -0
data/specs/bin/filter_and_validate__multiple_vals_helper.yaml +202 -0
data/specs/bin/filter_and_validate_spec.rb +124 -0
data/specs/bin/ms_to_lmat_spec.rb +34 -0
data/specs/bin/prob_validate_spec.rb +62 -0
data/specs/bin/protein_summary_spec.rb +10 -0
data/{test/tc_fasta.rb → specs/fasta_spec.rb} +354 -310
data/specs/gi_spec.rb +22 -0
data/specs/load_bin_path.rb +7 -0
data/specs/merge_deep_spec.rb +13 -0
data/specs/ms/gradient_program_spec.rb +77 -0
data/specs/ms/msrun_spec.rb +455 -0
data/specs/ms/parser_spec.rb +92 -0
data/specs/ms/spectrum_spec.rb +89 -0
data/specs/roc_spec.rb +251 -0
data/specs/rspec_autotest.rb +149 -0
data/specs/sample_enzyme_spec.rb +41 -0
data/specs/spec_helper.rb +133 -0
data/specs/spec_id/aa_freqs_spec.rb +52 -0
data/{test/tc_bioworks.rb → specs/spec_id/bioworks_spec.rb} +56 -71
data/specs/spec_id/digestor_spec.rb +75 -0
data/specs/spec_id/precision/filter/cmdline_spec.rb +20 -0
data/specs/spec_id/precision/filter/output_spec.rb +31 -0
data/specs/spec_id/precision/filter_spec.rb +243 -0
data/specs/spec_id/precision/prob_spec.rb +111 -0
data/specs/spec_id/precision/prob_spec_helper.rb +0 -0
data/specs/spec_id/proph/pep_summary_spec.rb +143 -0
data/{test/tc_proph.rb → specs/spec_id/proph/prot_summary_spec.rb} +52 -32
data/{test/tc_protein_summary.rb → specs/spec_id/protein_summary_spec.rb} +85 -0
data/specs/spec_id/sequest/params_spec.rb +68 -0
data/specs/spec_id/sequest/pepxml_spec.rb +452 -0
data/specs/spec_id/sqt_spec.rb +138 -0
data/specs/spec_id/srf_spec.rb +209 -0
data/specs/spec_id/srf_spec_helper.rb +302 -0
data/specs/spec_id_helper.rb +33 -0
data/specs/spec_id_spec.rb +361 -0
data/specs/spec_id_xml_spec.rb +33 -0
data/specs/transmem/phobius_spec.rb +423 -0
data/specs/transmem/toppred_spec.rb +297 -0
data/specs/transmem_spec.rb +60 -0
data/specs/transmem_spec_shared.rb +64 -0
data/specs/validator/aa_spec.rb +107 -0
data/specs/validator/background_spec.rb +51 -0
data/specs/validator/bias_spec.rb +146 -0
data/specs/validator/decoy_spec.rb +51 -0
data/specs/validator/fasta_helper.rb +26 -0
data/specs/validator/prot_from_pep_spec.rb +141 -0
data/specs/validator/transmem_spec.rb +145 -0
data/specs/validator/true_pos_spec.rb +58 -0
data/specs/validator_helper.rb +33 -0
data/specs/xml_spec.rb +12 -0
data/test_files/000_pepxml18_small.xml +206 -0
data/test_files/020a.mzXML.timeIndex +4710 -0
data/test_files/4-03-03_mzXML/000.mzXML.timeIndex +3973 -0
data/test_files/4-03-03_mzXML/020.mzXML.timeIndex +3872 -0
data/test_files/4-03-03_small-prot.xml +321 -0
data/test_files/4-03-03_small.xml +3876 -0
data/test_files/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
data/test_files/bioworks-3.3_10prots.xml +5999 -0
data/test_files/bioworks31.params +77 -0
data/test_files/bioworks32.params +62 -0
data/test_files/bioworks33.params +63 -0
data/test_files/bioworks_single_run_small.xml +7237 -0
data/test_files/bioworks_small.fasta +212 -0
data/test_files/bioworks_small.params +63 -0
data/test_files/bioworks_small.phobius +109 -0
data/test_files/bioworks_small.toppred.out +2847 -0
data/test_files/bioworks_small.xml +5610 -0
data/test_files/bioworks_with_INV_small.xml +3753 -0
data/test_files/bioworks_with_SHUFF_small.xml +2503 -0
data/test_files/corrupted_900.srf +0 -0
data/test_files/head_of_7MIX.srf +0 -0
data/test_files/interact-opd1_mods_small-prot.xml +304 -0
data/test_files/messups.fasta +297 -0
data/test_files/opd1/000.my_answer.100lines.xml +101 -0
data/test_files/opd1/000.tpp_1.2.3.first10.xml +115 -0
data/test_files/opd1/000.tpp_2.9.2.first10.xml +126 -0
data/test_files/opd1/000.v2.1.mzXML.timeIndex +3748 -0
data/test_files/opd1/000_020-prot.png +0 -0
data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml +62 -0
data/test_files/opd1/000_020_3prots-prot.xml +62 -0
data/test_files/opd1/opd1_cat_inv_small-prot.xml +139 -0
data/test_files/opd1/sequest.3.1.params +77 -0
data/test_files/opd1/sequest.3.2.params +62 -0
data/test_files/opd1/twenty_scans.mzXML +418 -0
data/test_files/opd1/twenty_scans.v2.1.mzXML +382 -0
data/test_files/opd1/twenty_scans_answ.lmat +0 -0
data/test_files/opd1/twenty_scans_answ.lmata +9 -0
data/test_files/opd1_020_beginning.RAW +0 -0
data/test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml +753 -0
data/test_files/orbitrap_mzData/000_cut.xml +1920 -0
data/test_files/pepproph_small.xml +4691 -0
data/test_files/phobius.small.noheader.txt +50 -0
data/test_files/phobius.small.small.txt +53 -0
data/test_files/s01_anC1_ld020mM.key.txt +25 -0
data/test_files/s01_anC1_ld020mM.meth +0 -0
data/test_files/small.fasta +297 -0
data/test_files/smallraw.RAW +0 -0
data/test_files/tf_bioworks2excel.bioXML +14340 -0
data/test_files/tf_bioworks2excel.txt.actual +1035 -0
data/test_files/toppred.small.out +416 -0
data/test_files/toppred.xml.out +318 -0
data/test_files/validator_hits_separate/bias_bioworks_small_HS.fasta +7 -0
data/test_files/validator_hits_separate/bioworks_small_HS.xml +5651 -0
data/test_files/yeast_gly_small-prot.xml +265 -0
data/test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes +6 -0
data/test_files/yeast_gly_small.xml +3807 -0
data/test_files/yeast_gly_small2.parentTimes +6 -0
metadata +273 -57
data/bin/filter.rb +0 -6
data/bin/precision.rb +0 -5
data/lib/spec/mzdata/parser.rb +0 -108
data/lib/spec/mzdata.rb +0 -48
data/lib/spec/mzxml/parser.rb +0 -449
data/lib/spec/scan.rb +0 -55
data/lib/spec_id/filter.rb +0 -797
data/lib/spec_id/precision.rb +0 -421
data/lib/toppred.rb +0 -18
data/script/filter-peps.rb +0 -164
data/test/tc_aa_freqs.rb +0 -59
data/test/tc_fasta_shaker.rb +0 -149
data/test/tc_filter.rb +0 -203
data/test/tc_filter_peps.rb +0 -46
data/test/tc_gi.rb +0 -17
data/test/tc_id_class_anal.rb +0 -70
data/test/tc_id_precision.rb +0 -89
data/test/tc_msrun.rb +0 -88
data/test/tc_mzxml.rb +0 -88
data/test/tc_mzxml_to_lmat.rb +0 -36
data/test/tc_peptide_parent_times.rb +0 -27
data/test/tc_precision.rb +0 -60
data/test/tc_roc.rb +0 -166
data/test/tc_sample_enzyme.rb +0 -32
data/test/tc_scan.rb +0 -26
data/test/tc_sequest.rb +0 -336
data/test/tc_spec.rb +0 -78
data/test/tc_spec_id.rb +0 -201
data/test/tc_spec_id_xml.rb +0 -36
data/test/tc_srf.rb +0 -262

data/specs/ms/spectrum_spec.rb ADDED Viewed

@@ -0,0 +1,89 @@
+require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
+require 'ms/spectrum'
+describe MS::Spectrum, 'equal_after_rounding?' do
+  before(:all) do
+    @spectrum = MS::Spectrum.new
+  end
+  it 'returns equal after rounding' do
+    [[123.32145, 123.32, true], [123.328, 123.32, false], [123, 124, false], [122.94532, 123, true], [123, 123, true], [6.233355, 6.2334, true], [1029.212890625, 1029.212891, true]].each do |ar|
+      (precise, less_precise, answ) = ar
+      @spectrum.equal_after_rounding?(precise.to_f, less_precise.to_f).should == answ
+    end
+  end
+end
+describe MS::Spectrum, 'with a few values' do
+  before(:each) do
+    @mz = [1.2, 4.23332, 5.345734, 6.233355, 7.889]
+    @spec = MS::Spectrum.new(@mz,Array.new(5,100))
+  end
+  it 'finds an index given an exact m/z' do
+    @mz.each_with_index do |x,i|
+      @spec.index(x).should == i
+    end
+    [1, 4.233, 5.346, 6.2334, 7.89].each_with_index do |x,i|
+      @spec.index(x).should == i
+    end
+  end
+  it 'index returns nil if the m/z does not exist' do
+    [0.9, 1.28, 0, -10, 100, 4.233322, 4.233310, 4.3, 8.001, 7.905].each_with_index do |x,i|
+      @spec.index(x).should == nil
+    end
+  end
+  it 'finds an index given a rounded m/z' do
+    [1, 4, 5, 6, 8].each_with_index do |x,i|
+      @spec.index(x).should == i
+    end
+  end
+end
+describe MS::Spectrum, 'of full values' do
+  before(:each) do
+    @spec = MS::Spectrum.new(Ref::MZ,Array.new(Ref::MZ.size,100))
+  end
+  it 'finds an index given an exact m/z' do
+    @spec.index(1121.91625976562).should == 665
+    @spec.index(1029.212890625).should == 597
+    #@spec.index(1029.212891).should == 665
+  end
+  it 'finds an index given approximate m/z' do
+    @spec.index(1121.91626).should == 665
+    @spec.index(1029.212891).should == 597
+  end
+end
+class Ref
+    MZ = [300.801086425781, 301.70166015625, 302.771240234375, 303.972473144531, 304.845275878906, 305.704711914062, 306.92919921875, 307.755126953125, 309.0087890625, 309.868713378906, 310.956420898438, 312.174194335938, 312.815185546875, 314.045654296875, 315.086730957031, 316.046752929688, 317.3525390625, 318.233642578125, 319.613647460938, 321.082092285156, 322.192321777344, 322.95458984375, 323.894653320312, 325.020385742188, 325.743286132812, 326.779418945312, 327.823303222656, 328.613891601562, 329.550903320312, 330.544738769531, 331.53125, 332.574829101562, 334.576965332031, 335.536254882812, 336.649353027344, 337.825805664062, 339.057189941406, 340.065063476562, 340.720581054688, 341.499572753906, 342.942199707031, 343.76025390625, 344.600280761719, 345.855041503906, 346.655639648438, 347.846435546875, 348.9169921875, 349.891235351562, 350.635437011719, 351.70458984375, 352.663940429688, 353.673217773438, 354.972717285156, 355.828247070312, 356.828125, 357.716613769531, 358.844848632812, 360.2294921875, 360.850402832031, 361.569580078125, 362.565002441406, 363.612182617188, 365.454711914062, 366.121337890625, 366.760559082031, 367.6083984375, 368.523986816406, 369.439453125, 370.830444335938, 371.803466796875, 372.514587402344, 374.044555664062, 374.806091308594, 375.821472167969, 377.040344238281, 377.854248046875, 378.756591796875, 379.71533203125, 380.576477050781, 381.725463867188, 382.475708007812, 383.616394042969, 384.813537597656, 386.129638671875, 387.6005859375, 388.932556152344, 390.297546386719, 391.094055175781, 392.089965820312, 392.823608398438, 394.235961914062, 394.960632324219, 395.694702148438, 396.635864257812, 397.776733398438, 399.250183105469, 400.538269042969, 401.433288574219, 402.387023925781, 402.995971679688, 403.692077636719, 404.801391601562, 405.716735839844, 406.731872558594, 408.219970703125, 409.398498535156, 410.421936035156, 411.209594726562, 412.011962890625, 412.739013671875, 413.435119628906, 414.143432617188, 415.083251953125, 416.492919921875, 417.629638671875, 418.542541503906, 419.22216796875, 419.897338867188, 420.7880859375, 421.839172363281, 422.86328125, 424.165710449219, 425.020263671875, 425.712097167969, 427.219360351562, 427.953247070312, 429.039367675781, 429.842346191406, 430.9833984375, 431.811462402344, 432.787719726562, 434.198486328125, 434.911071777344, 435.6279296875, 437.321166992188, 438.197448730469, 441.392822265625, 442.794372558594, 443.688232421875, 444.597534179688, 445.466247558594, 446.227966308594, 446.914245605469, 447.546936035156, 448.173278808594, 449.515563964844, 450.155517578125, 451.076049804688, 451.80859375, 452.888122558594, 454.161865234375, 455.119873046875, 456.791748046875, 457.733276367188, 458.702209472656, 459.986145019531, 460.669982910156, 461.494323730469, 462.233276367188, 463.476440429688, 464.808959960938, 465.488830566406, 466.521667480469, 467.236267089844, 468.25927734375, 469.573364257812, 470.788391113281, 471.397033691406, 472.3251953125, 473.016174316406, 473.884033203125, 474.768127441406, 475.71484375, 476.4599609375, 477.563171386719, 478.803833007812, 479.960021972656, 480.684143066406, 482.565612792969, 483.507568359375, 484.445495605469, 485.277221679688, 485.967590332031, 486.720397949219, 487.870178222656, 488.918029785156, 489.744018554688, 491.068664550781, 491.833435058594, 492.650573730469, 493.965026855469, 495.259765625, 496.394714355469, 497.059448242188, 498.060180664062, 499.154357910156, 501.302062988281, 502.07275390625, 504.229919433594, 505.106811523438, 505.800537109375, 508.017761230469, 508.681884765625, 509.696044921875, 510.333312988281, 512.247802734375, 513.393798828125, 514.066650390625, 515.622314453125, 516.840087890625, 518.3681640625, 519.65673828125, 521.18798828125, 521.8134765625, 522.556640625, 525.173583984375, 526.93017578125, 527.8955078125, 528.546630859375, 530.037109375, 530.682250976562, 531.6689453125, 533.123291015625, 534.359375, 535.144409179688, 535.915893554688, 537.208251953125, 537.831787109375, 538.450927734375, 539.700805664062, 540.919921875, 541.69873046875, 542.658203125, 544.65087890625, 546.431884765625, 547.52587890625, 549.49169921875, 551.28564453125, 552.2568359375, 554.173461914062, 554.998901367188, 555.777709960938, 556.683837890625, 557.781616210938, 558.829345703125, 559.62548828125, 561.412719726562, 566.22509765625, 568.303344726562, 569.317138671875, 570.64501953125, 571.35302734375, 572.68603515625, 573.504028320312, 574.764892578125, 576.551025390625, 578.062744140625, 579.164184570312, 579.979125976562, 580.649169921875, 581.505859375, 582.594116210938, 583.317016601562, 583.935546875, 584.800659179688, 585.533325195312, 586.652099609375, 588.186767578125, 589.5595703125, 591.04345703125, 593.177368164062, 594.206787109375, 595.06591796875, 595.67822265625, 596.616333007812, 598.947021484375, 599.933471679688, 601.442138671875, 602.24853515625, 603.02880859375, 604.325927734375, 605.169189453125, 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+end

data/specs/roc_spec.rb ADDED Viewed

@@ -0,0 +1,251 @@
+require File.expand_path( File.dirname(__FILE__) + '/spec_helper'
 )
+require 'roc'
+describe 'an area under the curve calculator', :shared => true do
+  it 'calculates area under curve correctly' do
+    x_y_pairs = {
+      [[1,2,3],[2,3,4]]    => 6,
+      [[1,2,3],[-2,-3,-4]] => -6,
+      [[1,2,3],[4,3,2]]    => 6,
+      [[1,2,3],[-4,-3,-2]] => -6,
+      [[4,5,6],[2,1,2]]    => 3,
+      [[4,5,6],[-2,-1,-2]] => -3,
+    }
+    x_y_pairs.each do |k,v|
+      calculate(*k).should == v
+    end
+  end
+  def calculate(x,y)
+    @method.call(x,y)
+  end
+end
+describe ROC do
+  before(:all) do
+    @method = proc {|x,y| ROC.new.area_under_curve(x,y) }
+  end
+  it_should_behave_like 'an area under the curve calculator'
+  it 'gives doublets_to_separate' do
+    t = true
+    f = false
+    x,y = ROC.new.doublets_to_separate([[0,f],[1,f],[2,f],[3,t],[3,f],[0,f],[4,f],[1,t],[2,t]])
+    x.should == [1,2,3]
+    y.should == [0,0,1,2,3,4]
+  end
+  it 'gives tps_and_ppv' do
+    tp = %w(1 2 3 4 5 6 6 6 7 8 9 10 10 10 10 11 12 ).collect {|c| c.to_f } # 17 total
+    fp = %w(3.5 4 5 5 5 6 6 6.5 7 8 9 9.5 10 15).collect {|c| c.to_f } # 14 total
+    xe = [1, 2, 3, 4, 5, 8, 9, 10, 11, 15, 16, 17]
+    #       1, 2, 3, 4        5,   6,             7,             8,   9
+    #       10              11                12
+    ye = [1, 1, 1, 4.0/6.0, 0.5, 8.0/(7.0+8.0), 9.0/(9.0+9.0), 0.5, 11.0/(11.0+ 11.0),  15.0/(15.0+13.0), 16.0/(16.0+13.0), 17.0/(17.0+13.0)]
+    _test_tps_and_ppv_method(tp,fp,xe,ye,"complex real-life-like scenario")
+    ## leading fp's
+    tp = [1,2,3]
+    fp = [0,0,1,2,3,4]
+    xe = [1,2,3]
+    ye = [1.0/(1+3), 2.0/(2+4), 3.0/(3+5)]
+    _test_tps_and_ppv_method(tp,fp,xe,ye, "leading fps")
+    ## leading tp's
+    tp = [-1,2,3]
+    fp = [0,4]
+    xe = [1,2,3]
+    ye = [1.0/(1+0), 2.0/(2+1), 3.0/(3+1)]
+    _test_tps_and_ppv_method(tp,fp,xe,ye, "leading tps")
+    ## equal tp's leading
+    tp = [0.0001,0.0001,0.0001,2]
+    fp = [0.01,4.0]
+    xe = [3,4]
+    ye = [3.0/(3+0), 4.0/(4+1)]
+    _test_tps_and_ppv_method(tp,fp,xe,ye, "equal tps leading")
+    ## equal arrays with some repeated values
+    tp = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
+    fp = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
+    xe = [1,2,4,5,6,7]
+    ye = [0.5, 0.5, 0.5, 0.5, 0.5, 0.5]
+    _test_tps_and_ppv_method(tp,fp,xe,ye, "equal arrays with some repeated values")
+  end
+  it 'gives numhits_and_ppv' do
+    ## leading fp's
+    tp = [1,2,3]
+    fp = [0,0,1,2,3,4]
+    xe = [2,4,6,8,9]
+    ye = [0.0/2, 1.0/4, 2.0/6, 3.0/8, 3.0/9]
+    _test_numhits_and_ppv_method(tp,fp,xe,ye, "leading fps")
+    ## leading tp's
+    tp = [-1,2,3]
+    fp = [0,4]
+    xe = [1, 2, 3, 4, 5]
+    ye = [1.0/1, 1.0/2, 2.0/3, 3.0/4, 3.0/5]
+    _test_numhits_and_ppv_method(tp,fp,xe,ye, "leading tps")
+    ## equal tp's leading
+    tp = [0.0001,0.0001,0.0001,2]
+    fp = [0.01,4.0]
+    xe = [3, 4, 5, 6]
+    ye = [3.0/3, 3.0/4, 4.0/5, 4.0/6]
+    _test_numhits_and_ppv_method(tp,fp,xe,ye, "equal tps leading")
+    ## equal arrays with some repeated values
+    tp = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
+    fp = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
+    xe = [2, 4, 8, 10, 12, 14]
+    ye = [0.5, 0.5, 0.5, 0.5, 0.5, 0.5]
+    _test_numhits_and_ppv_method(tp,fp,xe,ye, "equal arrays with some repeated values")
+    ## @TODO: NEED TO FILL THIS OUT!
+=begin
+    tp = %w(1 2 3 4 5 6 6 6 7 8 9 10 10 10 10 11 12 ).collect {|c| c.to_f } # 17 total
+    fp = %w(3.5 4 5 5 5 6 6 6.5 7 8 9 9.5 10 15).collect {|c| c.to_f } # 14 total
+    xe = [1, 2, 3, 4, ]
+    #       1, 2, 3, 4        5,   6,             7,             8,   9
+    #       10              11                12
+    ye = [1, 1, 1, 4.0/6.0, 0.5, 8.0/(7.0+8.0), 9.0/(9.0+9.0), 0.5, 11.0/(11.0+ 11.0),  15.0/(15.0+13.0), 16.0/(16.0+13.0), 17.0/(17.0+13.0)]
+    _test_tps_and_ppv_method(tp,fp,xe,ye,"complex real-life-like scenario")
+=end
+  end
+  def _test_numhits_and_ppv_method(tp,fp,xe,ye,message='')
+    roc = ROC.new
+    list = roc.separate_to_doublets(tp,fp)
+    (x,y) = roc.numhits_and_ppv(list)
+    y.size.should == x.size
+    x.should == xe
+    y.should == ye
+  end
+  def _test_tps_and_ppv_method(tp,fp,xe,ye,message='')
+    (x,y) = ROC.new.tps_and_ppv(tp,fp)
+    y.size.should == x.size
+    x.should == xe
+    y.should == ye
+  end
+end
+describe DecoyROC do
+  ###################################################################
+  it 'gives pred_and_ppv' do
+    hits = [1,2,3]
+    decoys = [0,0,1,2,3,4]
+    num_hits_e = [1,2,3]
+    num_fps = [3,4,5]
+    # expected = [-2.0/1, -2.0/2, -2.0/3]
+    _test_pred_and_ppv(hits, decoys, num_hits_e, num_fps)
+  end
+  it 'gives pred_tps_ppv__leading_tps' do
+    ## leading tp's
+    hits = [-1,2,3]
+    decoys = [0,4]
+    num_hits_e = [1,2,3]
+    num_fps = [0,1,1]
+    _test_pred_and_ppv(hits, decoys, num_hits_e, num_fps)
+  end
+  it 'gives pred_tps_ppv__equal_tps_leading' do
+    hits = [0.0001,0.0001,0.0001,2]
+    decoys = [0.01,4.0]
+    num_hits_e = [3,4]
+    num_fps = [0,1]
+    _test_pred_and_ppv(hits, decoys, num_hits_e, num_fps)
+  end
+  it 'gives pred_tps_ppv__equal_arrays_with_some_repeated_values' do
+    hits = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
+    decoys = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
+    num_hits_e = [1,2,4,5,6,7]
+    num_fps = [1,2,4,5,6,7]
+    _test_pred_and_ppv(hits, decoys, num_hits_e, num_fps)
+  end
+  ###################################################################
+  it 'gives pred_tps_ppv__leading_fps' do
+    ## leading fp's
+    hits = [1,2,3]
+    decoys = [0,0,1,2,3,4]
+    num_hits_e = [1,2,3]
+    num_fps = [3,4,5]
+    tps_e = make_tps_e(num_fps, num_hits_e)
+    ppv_e = make_ppv_e(tps_e, num_hits_e)
+    _test_pred_and_tps_and_ppv(hits, decoys, num_hits_e, tps_e, ppv_e)
+  end
+  it 'gives pred_tps_ppv__leading_tps' do
+    ## leading tp's
+    hits = [-1,2,3]
+    decoys = [0,4]
+    num_hits_e = [1,2,3]
+    num_fps = [0,1,1]
+    tps_e = make_tps_e(num_fps, num_hits_e)
+    ppv_e = make_ppv_e(tps_e, num_hits_e)
+    _test_pred_and_tps_and_ppv(hits, decoys, num_hits_e, tps_e, ppv_e)
+  end
+  it 'gives pred_tps_ppv__equal_tps_leading' do
+    hits = [0.0001,0.0001,0.0001,2]
+    decoys = [0.01,4.0]
+    num_hits_e = [3,4]
+    num_fps = [0,1]
+    tps_e = make_tps_e(num_fps, num_hits_e)
+    ppv_e = make_ppv_e(tps_e, num_hits_e)
+    _test_pred_and_tps_and_ppv(hits, decoys, num_hits_e, tps_e, ppv_e)
+  end
+  it 'gives pred_tps_ppv__equal_arrays_with_some_repeated_values' do
+    hits = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
+    decoys = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
+    num_hits_e = [1,2,4,5,6,7]
+    num_fps = [1,2,4,5,6,7]
+    tps_e = make_tps_e(num_fps, num_hits_e)
+    ppv_e = make_ppv_e(tps_e, num_hits_e)
+    _test_pred_and_tps_and_ppv(hits, decoys, num_hits_e, tps_e, ppv_e)
+  end
+  def  _test_pred_and_ppv(hits, decoys, num_hits_e, num_fps)
+    answer = DecoyROC.new.pred_and_ppv(hits, decoys)
+    precision = num_hits_e.zip(num_fps).map do |h,f|
+      (h - f).to_f / h
+    end
+    answer.should == [num_hits_e, precision]
+  end
+  def _test_pred_and_tps_and_ppv(hits, decoys, num_hits_e, tps_e, ppv_e)
+    answer = DecoyROC.new.pred_and_tps_and_ppv(hits, decoys)
+    expected = [num_hits_e, tps_e, ppv_e]
+    %w(num_hits num_tps ppv).each_with_index do |cat, i|
+      answer[i].should == expected[i]
+    end
+  end
+  def make_tps_e(num_fps, num_hits_e)
+    tps_e = []
+    num_hits_e.each_with_index do |v,i|
+      tps_e[i] = v - num_fps[i]
+    end
+    tps_e
+  end
+  def make_ppv_e(tps_e, num_hits_e)
+    ppv_e = []
+    tps_e.each_with_index {|v,i| ppv_e[i] = v.to_f/num_hits_e[i] }
+    ppv_e
+  end
+end

data/specs/rspec_autotest.rb ADDED Viewed

@@ -0,0 +1,149 @@
+# (c) Copyright 2006-2007 Nick Sieger <nicksieger@gmail.com>
+#
+# Permission is hereby granted, free of charge, to any person
+# obtaining a copy of this software and associated documentation files
+# (the "Software"), to deal in the Software without restriction,
+# including without limitation the rights to use, copy, modify, merge,
+# publish, distribute, sublicense, and/or sell copies of the Software,
+# and to permit persons to whom the Software is furnished to do so,
+# subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be
+# included in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+require 'rubygems'
+gem 'ZenTest'
+require 'autotest'
+class RspecAutotest < Autotest
+  attr_accessor :spec_command
+  def initialize # :nodoc:
+    @spec_command = "spec --diff unified"
+    super
+    @exceptions = %r%^\./(?:coverage|doc)%
+  end
+  def tests_for_file(filename)
+    case filename
+    when /^lib\/.*\.rb$/ then
+      impl = File.basename(filename).gsub('_', '_?').sub(/\.rb$/, '')
+      @files.keys.select do |k|
+        k =~ %r%^spec/.*#{impl}_spec\.rb$%
+      end
+    when %r%^spec/spec_helper.rb% then
+      @files.keys.select do |f|
+        f =~ %r%^spec/.*_spec\.rb$%
+      end
+    when /^spec\/.*_spec\.rb$/ then
+      [filename]
+    when /#{Regexp.quote(File.basename(__FILE__))}/
+      # Don't respond to changes to this file
+      []
+    else
+      @output.puts "Dunno! #{filename}" if $TESTING
+      []
+    end
+  end
+  def handle_results(results)
+    failed = results.scan(/^\d+\)\n(?:\e\[\d*m)?(?:.*?Error in )?'([^\n]*)'(?: FAILED)?(?:\e\[\d*m)?\n(.*?)\n\n/m)
+    @files_to_test = consolidate_failures failed
+    unless @files_to_test.empty? then
+      hook :red
+    else
+      hook :green
+    end unless $TESTING
+    @tainted = true unless @files_to_test.empty?
+  end
+  def consolidate_failures(failed)
+    filters = Hash.new { |h,k| h[k] = [] }
+    failed.each do |spec, failed_trace|
+      @files.keys.select{|f| f =~ /spec\//}.each do |f|
+        if failed_trace =~ Regexp.new(f)
+          filters[f] << spec
+          break
+        end
+      end
+    end
+    return filters
+  end
+  def make_test_cmd(files_to_test)
+    cmds = []
+    full, partial = files_to_test.partition { |k,v| v.empty? }
+    unless full.empty? then
+      classes = full.map {|k,v| k}.flatten.join(' ')
+      cmds << "#{spec_command} #{classes}"
+    end
+    partial.each do |klass, methods|
+      methods.each { |meth| cmds << "#{spec_command} -s #{meth.inspect} #{klass}" }
+    end
+    return cmds.join('; ')
+  end
+end
+class RspecOnRailsAutotest < RspecAutotest
+  def initialize # :nodoc:
+    super
+    @exceptions = %r%^\./(?:coverage|db|doc|log|public|script|vendor)%
+  end
+  def tests_for_file(filename)
+    case filename
+    when %r%^spec/fixtures/(.*)s.yml% then
+      ["spec/models/#{$1}_spec.rb",
+       "spec/controllers/#{$1}_controller_spec.rb"]
+    when %r%^spec/models/.*rb$% then
+      [filename]
+    when %r%^spec/controllers/.*\.rb$% then
+      [filename]
+    when %r%^spec/views/.*\.rb$% then
+      [filename]
+    when %r%^spec/helpers/.*\.rb$% then
+      [filename]
+    when %r%^app/models/(.*)\.rb$% then
+      ["spec/models/#{$1}_spec.rb"]
+    when %r%^app/helpers/application_helper.rb% then
+      @files.keys.select { |f|
+        f =~ %r%^spec/controllers/.*_spec\.rb$%
+      }
+    when %r%^app/helpers/(.*)_helper.rb% then
+      ["spec/controllers/#{$1}_controller_spec.rb", "spec/helpers/#{$1}_spec.rb"]
+    when %r%^app/controllers/application.rb$% then
+      @files.keys.select { |f|
+        f =~ %r%^spec/controllers/.*_spec\.rb$%
+      }
+    when %r%^app/controllers/(.*)\.rb$% then
+      ["spec/controllers/#{$1}_spec.rb"]
+    when %r%^app/views/layouts/% then
+      []
+    when %r%^app/views/(.*)/% then
+      ["spec/controllers/#{$1}_controller_spec.rb", "spec/views/#{$1}_spec.rb"]
+    when %r%^config/routes.rb$% then
+      @files.keys.select do |f|
+        f =~ %r%^spec/controllers/.*_spec\.rb$%
+      end
+    when %r%^spec/spec_helper.rb%,
+         %r%^config/((boot|environment(s/test)?).rb|database.yml)% then
+      @files.keys.select do |f|
+        f =~ %r%^spec/(models|controllers)/.*_spec\.rb$%
+      end
+    else
+      @output.puts "Dunno! #{filename}" if $TESTING
+      []
+    end.uniq.select { |f| @files.has_key? f }
+  end
+end

data/specs/sample_enzyme_spec.rb ADDED Viewed

@@ -0,0 +1,41 @@
+require File.expand_path( File.dirname(__FILE__) + '/spec_helper' )
+require 'sample_enzyme'
+require 'set'
+describe SampleEnzyme, "digesting sequences" do
+  it 'can digest with no missed cleavages' do
+    st = "CRGATKKTAGRPMEK"
+    SampleEnzyme.tryptic(st).should == %w(CR GATK K TAGRPMEK)
+    st = "CATRP"
+    SampleEnzyme.tryptic(st).should == %w(CATRP)
+    st = "RCATRP"
+    SampleEnzyme.tryptic(st).should == %w(R CATRP)
+    st = ""
+    SampleEnzyme.tryptic(st).should == []
+    st = "R"
+    SampleEnzyme.tryptic(st).should == %w(R)
+  end
+  it 'can digest with missed cleavages' do
+    st = "CRGATKKTAGRPMEKLLLERTKY"
+    zero = %w(CR GATK K TAGRPMEK LLLER TK Y)
+    SampleEnzyme.tryptic(st,0).to_set.should == zero.to_set
+    one = %w(CRGATK GATKK KTAGRPMEK TAGRPMEKLLLER LLLERTK TKY)
+    SampleEnzyme.tryptic(st,1).to_set.should == (zero+one).to_set
+    two = %w(CRGATKK GATKKTAGRPMEK KTAGRPMEKLLLER TAGRPMEKLLLERTK LLLERTKY)
+    all = zero + one + two
+    SampleEnzyme.tryptic(st,2).to_set.should == all.to_set
+  end
+  it 'contains duplicates IF there are duplicate tryptic sequences' do
+    st = "AAAAKCCCCKDDDDKCCCCK"
+    peps = SampleEnzyme.new('trypsin').digest(st, 2)
+    peps.select {|aaseq| aaseq == 'CCCCK'}.size.should == 2
+  end
+end

data/specs/spec_helper.rb ADDED Viewed

@@ -0,0 +1,133 @@
+gem 'rspec'
+# a global flag that lets me know what format we're dealing with for output
+$specdoc = false
+ObjectSpace.each_object do |obj|
+  case obj
+  when Spec::Runner::Formatter::SpecdocFormatter
+    $specdoc = true
+  end
+end
+# Set up some global testing variables:
+#silent {
+  ROOT_DIR = File.dirname(__FILE__) + '/..'
+  SPEC_DIR = File.dirname(__FILE__)
+  Tfiles = File.dirname(__FILE__) + '/../test_files'
+  Tfiles_l = File.dirname(__FILE__) + '/../test_files_large'
+  Tfiles_large = Tfiles_l
+#}
+# this variable is for large files!
+if ENV['SPEC_LARGE']
+  $spec_large = true
+else
+  #[NOTE: NOT testing with large test files]"
+  # ** run with env var: SPEC_LARGE and ensure tfiles_large dir"
+  $spec_large = false
+end
+def spec_large(&block)
+  if $spec_large
+    block.call
+  else
+    # Requires SPEC_LARGE=true and tfiles_large dir for testing large test files
+    it 'SKIPPING (not testing large files)' do
+    end
+  end
+end
+# returns all output to stdout as a string
+# will respond to is_a? File -> false is_a? IO true even though it is really a
+# file
+def capture_stdout(&block)
+  capture_file = Tfiles + '/capture_stdout.tmp'
+  def capture_file.is_a?(klass)
+    case klass.to_s
+    when 'IO'
+      true
+    when 'File'
+      false
+    else
+      false
+    end
+  end
+  $stdout = File.open(capture_file, 'w')
+  block.call
+  $stdout.close
+  $stdout = STDOUT
+  string = IO.read(capture_file)
+  File.unlink capture_file
+  string
+end
+require 'ostruct'
+# class for using a ruby-ish initializer
+class MyOpenStruct < OpenStruct
+  def initialize(*args)
+    super(*args)
+    if block_given?
+      yield(self)
+    end
+  end
+end
+def xdescribe(*args)
+  puts "describe: #{args.join(' ')}"
+  puts "**SKIPPING**"
+end
+def Xdescribe(*args)
+  xdescribe(*args)
+end
+def xit(*args)
+  puts "\n- SKIPPING: #{args.join(' ')}"
+end
+def it_should(*args)
+  string = "- WRITE TEST: #{args.join(' ')}"
+  if $specdoc
+    puts(string)
+  else
+    puts("\n" + string)
+  end
+end
+def silent(&block)
+  tmp = $VERBOSE ; $VERBOSE = nil
+  block.call
+  $VERBOSE = tmp
+end
+require SPEC_DIR + '/load_bin_path'
+class String
+  #alias_method :exist?, exist_as_a_file?
+  #alias_method exist_as_a_file?, exist?
+  def exist?
+    File.exist? self
+  end
+  def exist_as_a_file?
+    File.exist? self
+  end
+end
+describe "a cmdline program", :shared => true do
+  before(:all) do
+    testdir = File.dirname(__FILE__)
+    libdir = testdir + '/../lib'
+    bindir = testdir +  '/../bin'
+    @cmd = "ruby -I #{libdir} #{bindir}/#{@progname} "
+  end
+  it 'gives usage when called with no args' do
+    reply = `#{@cmd}`
+    reply.should =~ /usage/i
+  end
+end