mspire 0.4.9 → 0.5.0

data/specs/fasta_spec.rb

@@ -1,354 +0,0 @@
-require File.expand_path( File.dirname(__FILE__) + '/spec_helper' )
-
-require 'fasta'
-
-Filestring = ">gi|P1
-AMKRGAN
->gi|P2
-CRGATKKTAGRPMEK
->gi|P3
-PEPTIDE
-"
-
-class Fasta
-  def proteins?
-    (@prots.size > 0) and
-    @prots.first.is_a? Fasta::Prot
-  end
-end
-
-describe Fasta do
-
-  it 'can be set from a string' do
-    obj = Fasta.from_string(Filestring)
-    obj.is_a?(Fasta).should be_true
-    obj.proteins?.should be_true
-    obj.size.should == 3
-    matches_filestring(obj)
-  end
-
-  # given a fasta obj, asks if it matches filestring
-  def matches_filestring(obj)
-    heads = %w(>gi|P1 >gi|P2 >gi|P3)
-    seqs = %w(AMKRGAN CRGATKKTAGRPMEK PEPTIDE)
-    obj.zip(heads, seqs) do |prot, head, seq|
-      prot.header.should == head
-      prot.aaseq.should == seq
-    end
-  end
-
-end
-
-describe Fasta::Prot do
-
-  it 'can extract a gi code out of ncbi sequences' do
-    gis = ['>gi|7427923|pir||PHRBG glycogen phosphorylase (EC 2.4.1.1), muscle - rabbit', '>sp|lollygag|helloyou', '>only has one bar | and thats it', 'notme|me|nome', '>lots|an|lots|of|bars|heehee']
-    answ = ['7427923', 'lollygag', nil, 'me','an']
-    actual = gis.map do |head|
-      Fasta::Prot.new(head).gi
-    end
-    actual.should == answ
-  end
-end
-
-=begin
-
-require File.dirname(File.expand_path(__FILE__)) + '/load_bin_path'
-require 'test/unit'
-require 'fasta'
-require 'assert_files'
-require 'sample_enzyme'
-require 'set'
-
-
-module Test::Unit::Assertions
-  @@file_display_length = 10000
-end
-
-class FastaTest < Test::Unit::TestCase
-  NODELETE = false
-
-  def initialize(arg)
-    super(arg)
-
-    @cat_shuffle_postfix = Fasta::CAT_SHUFF_FILE_POSTFIX
-    @connector = Fasta::FILE_CONNECTOR
-    @shuff_prefix = Fasta::SHUFF_PREFIX
-    @inv_prefix = Fasta::SHUFF_PREFIX
-    @shuff_ext = Fasta::SHUFF_FILE_POSTFIX
-    @inv_ext = Fasta::INV_FILE_POSTFIX
-
-    @tfiles = File.dirname(__FILE__) + '/tfiles/'
-    @base_cmd = "ruby -I #{File.join(File.dirname(__FILE__), "..", "lib")} -S "
-    @fasta_mod_cmd = @base_cmd + "fasta_mod.rb "
-    @fasta_cat_mod_cmd = @base_cmd + "fasta_cat_mod.rb "
-    @fasta_cat_cmd = @base_cmd + "fasta_cat.rb "
-    @sf = @tfiles + "small.fasta"
-    @sf_shuffle = @tfiles + "small#{@shuff_ext}.fasta"
-    @sf_invert = @tfiles + "small#{@inv_ext}.fasta"
-    @sf_cat = @tfiles + "small__small_SHUFF.fasta"
-    @sf_cat_mod = @tfiles + "small#{@cat_shuffle_postfix}.fasta"
-    @mf = @tfiles + "messups.fasta"
-  end
-
-  def test_read_file
-    obj = Fasta.new.read_file(@sf)
-    @tmpfile = @tfiles + "tmp.tmp"
-    obj.write_file(@tmpfile)
-    assert_not_equal_file_content(@tmpfile, @sf)
-    obj2 = Fasta.new.read_file(@tmpfile)
-    File.unlink(@tmpfile)
-    assert_equal(obj, obj2)
-  end
-
-  def test_cat
-    obj = Fasta.new.read_file(@sf)
-    first_size = obj.prots.size
-    obj << obj
-    assert_equal(2, obj.prots.size/first_size)
-  end
-
-  def test_dup
-    obj = Fasta.new.read_file(@sf)
-    objd = obj.dup
-    obj_prots = obj.prots
-    objd.prots.each do |prot|
-      assert(obj_prots.include?(prot))
-    end
-  end
-
-  def test_prefix_extension
-    assert('f_howdy.ext', Fasta.prefix_extension('f.ext', '_howdy'))
-    assert('f.ext_howdy.ext', Fasta.prefix_extension('f.ext.ext', '_howdy'))
-  end
-
-  def test_cat_filenames
-    assert('f1f2.ext1', Fasta.cat_filenames(['f1.ext1', 'f2.ext2']))
-    assert('f1__f2.ext1', Fasta.cat_filenames(['f1.ext1', 'f2.ext2'], '__'))
-  end
-
-  def test_mod
-    ## Testing shuffle:
-    `#{@fasta_mod_cmd + 'shuffle ' + @sf}`
-    assert(File.exist?(@sf_shuffle), "output file #{@sf_shuffle} exists")
-    ob1 = Fasta.new.read_file(@sf)
-    ob2 = Fasta.new.read_file(@sf_shuffle)
-    assert_not_equal_file_content(@sf_shuffle, @sf)
-    File.unlink @sf_shuffle
-    assert(_same_headers?(ob1,ob2))
-    assert(_are_shuffled?(ob1,ob2))
-
-    ## Testing invert:
-    `#{@fasta_mod_cmd + 'invert ' + @sf}`
-    assert(File.exist?(@sf_invert), "output file #{@sf_invert} exists")
-    ob1 = Fasta.new.read_file(@sf)
-    ob2 = Fasta.new.read_file(@sf_invert)
-    assert_not_equal_file_content(@sf_invert, @sf)
-    File.unlink(@sf_invert)
-    assert(_same_headers?(ob1,ob2))
-    assert(_are_inverted?(ob1,ob2))
-
-    ## Testing prefix
-    #puts "#{@fasta_mod_cmd + '-p _HELLO_ invert ' + @sf}"
-    `#{@fasta_mod_cmd + 'invert -p _HELLO_ ' + @sf}` # NOT WORKING!
-    assert(File.exist?(@sf_invert), "output file #{@sf_invert} exists")
-    ob1 = Fasta.new.read_file(@sf)
-    ob2 = Fasta.new.read_file(@sf_invert)
-    assert(_are_inverted?(ob1,ob2))
-    assert_equal(ob1.prots.size, IO.read(@sf_invert).scan(/>_HELLO_/).size)
-    File.unlink(@sf_invert)
-  end
-
-  ## IN PROGRESS:
-  def Xtest_cat_mod
-
-    assert(File.exist?(@sf), "prerequisite for cat tests")
-
-    ## Single file to cat shuffle test
-    puts `#{@fcat_mod_cmd + @sf}`
-    assert(File.exist?(@sf_cat_single), "output file exists")
-    ob1 = Fasta.new.read_file(@sf)
-    ob2 = Fasta.new.read_file(@sf_cat_single)
-    assert_equal(2, ob2.prots.size/ob1.prots.size)
-    assert_equal(ob1.prots, ob2.prots[0, (ob1.prots.size)])
-    assert_not_equal(ob1.prots, ob2.prots[(ob1.prots.size)..-1])
-    File.unlink @sf_cat_single
-  end
-
-  ## IN PROGRESS:
-  def Xtest_cat
-
-    ## Concatenate files test:
-    puts `#{@cat_cmd + @sf} -p ,#{@shuff_prefix} #{@sfn}`
-    assert(File.exist?(@sf_cat), "output file #{@sf_cat} exists")
-    ob1 = Fasta.new.read_file(@sf)
-    ob2 = Fasta.new.read_file(@sfn)
-    ob3 = Fasta.new.read_file(@sf_cat)
-    assert_not_equal_file_content(@sf_cat, @sf)
-    assert_not_equal_file_content(@sf_cat, @sfn)
-    [@sfn,@sf_cat].each { |f| File.unlink f }
-
-    ob2.header_prefix!(@shuff_prefix)
-    ob3_prots = ob3.prots
-    [ob1, ob2].each do |ob|
-      ob.prots.each do |prot|
-        unless ob3_prots.include? prot
-          p prot
-          flunk "protein not found in cat version"
-        end
-      end
-    end
-
-
-    # test catenation
-    sfci = "small_CAT_INV.fasta"
-    cat_inverted = @tfiles + sfci
-    iccmd = @base_cmd + "fasta_cat_inverse.rb "
-    cmd = iccmd + @sf
-    puts `#{cmd}`
-    assert(File.exist?(cat_inverted), "file #{cat_inverted} exists")
-
-    norm = Fasta.new.read_file(@sf)
-    cat_inv = Fasta.new.read_file(cat_inverted)
-    File.unlink(cat_inverted)
-
-    num_prots = norm.prots.size
-    cat_norm_prots = cat_inv.prots[0, num_prots]
-    cat_inv_prots = cat_inv.prots[num_prots..-1]
-    norm.prots.each_with_index do |prot,i|
-      assert_equal(prot.header, cat_norm_prots[i].header)
-      assert_not_equal(prot.header, cat_inv_prots[i].header)
-      assert_equal(prot.aaseq, cat_norm_prots[i].aaseq) 
-      assert_equal(prot.aaseq.reverse!, cat_inv_prots[i].aaseq) 
-    end
-  end
-
-  def test_invert_tryptic_peptides
-    # FOR INDIVIDUAL PROTEINS:
-    seq = 'ABCKCDERDEKDGEKWXYRRKDER'
-    # tryptic = ABCK, CDER, DEK, DGEK, WXYR, R, K, DER
-    tryp = SampleEnzyme.tryptic(seq)
-    reverse_tryptic = %w(CBAK EDCR EDK EGDK YXWR R K EDR)
-    prot = Fasta::Prot.new(nil, seq)
-    prot.invert_tryptic_peptides!
-    assert_equal(reverse_tryptic.join(''), prot.aaseq, "reversing tryptic peptides")
-
-    seq = 'XYRABCD'
-    prot = Fasta::Prot.new(nil, seq)
-    prot.invert_tryptic_peptides!
-    assert_equal('YXRDCBA', prot.aaseq, 'last peptide treated special')
-
-    seq = 'XYRPABCD'
-    prot = Fasta::Prot.new(nil, seq)
-    prot.invert_tryptic_peptides!
-    assert_equal('DCBAPRYX', prot.aaseq, 'with a proline')
-    
-  end
-
-  def test_fraction_of_prots
-    peps = [['>silly1', "PEPTIDE"], ['>silly2', "ANOTHER"], ['>silly3', "AGAIN"], ['>silly4', "LARMA"]]
-    prots = peps.map do |header, seq|
-      Fasta::Prot.new(header, seq)
-    end
-    f = Fasta.new(prots)
-    # simple:
-    n = f.fraction_of_prots(1.0)
-    assert_equal(f.prots.map{|v| v.header }.to_set, n.prots.map{|v| v.header }.to_set, "same headers")
-    assert_equal(f.prots.map{|v| v.aaseq }.to_set, n.prots.map{|v| v.aaseq }.to_set, "same aaseqs")
-
-    pre = proc {|cnt| "SHUFF_f#{cnt}_" }
-    # test prefix
-    n = f.fraction_of_prots(1.0, pre)
-    n.prots.each do |prot|
-      assert_match(/^>SHUFF_f0_/, prot.header, "contains new prefix")
-    end
-
-    # smaller
-    n = f.fraction_of_prots(0.75, pre)
-    assert_equal(3, n.prots.size, "correct number of proteins")
-    # bigger
-    n = f.fraction_of_prots(2.5, pre)
-    assert_equal(10, n.prots.size, "correct number of proteins")
-    n.prots[0..3].each {|prt| assert_match(/^>SHUFF_f0_/, prt.header ) }
-    n.prots[4..7].each {|prt| assert_match(/^>SHUFF_f1_/, prt.header ) }
-    n.prots[8..9].each {|prt| assert_match(/^>SHUFF_f2_/, prt.header ) }
-    # crazy
-    n = f.fraction_of_prots(1.33, pre)
-    assert_equal(6, n.prots.size, "correct number of proteins")
-  end
-
-  def test_inverted_tryptic_peptides_for_file
-    # for a file:
-    tmpfile = @tfiles + "fasta.tmp"
-    fasta = Fasta.new.read_file(@sf)
-    fasta.aaseq_invert_tryptic_peptides!
-    fasta.write_file(tmpfile)
-    lines = IO.readlines(tmpfile)
-    #normal = 'MKRISTTITTTITITTGNGAG'
-    inverted_tryptic = 'MKRGAGNGTTITITTTITTSI' ## ?????
-    assert_equal(inverted_tryptic, lines[1].chomp)
-    #normal =  'MATYLIGDVHGCYDELIALLHKVEFTPGKDTLWLTGDLVARGPGSLDVLRYVKSLGDSVRLVLGNHDLHL
-    # LAVFAGISRNKPKDRLTPLLEAPDADELLNWLRRQPLLQIDEEKKLVMAHAGITPQWDLQTAKECARDVE
-    # AVLSSDSYPFFLDAMYGDMPNNWSPELRGLGRLRFITNAFTRMRFCFPNGQLDMYSKESPEEAPAPLKPW
-    # FAIPGPVAEEYSIAFGHWASLEGKGTPEGIYALDTGCCWGGTLTCLRWEDKQYFVQPSNRHKDLGEAAAS'
-    inverted_tryptic = 'HLLAILEDYCGHVDGILYTAMKGPTFEVKAVLDGTLWLTDRLVDLSGPGRVYKVSDGLSRSIGAFVALLHLDHNGLVLRPKNKDRLWNLLEDADPAELLPTLRREEDIQLLPQKKATQLDWQPTIGAHAMVLKACERLEPSWNNPMDGYMADLFFPYSDSSLVAEVDRGLGRLRTFANTIFRMRSYMDLQGNPFCFKGELSAWHGFAISYEEAVPGPIAFWPKLPAPAEEPSEKLCTLTGGWCCGTDLAYIGEPTGRDEWKNSPQVFYQRHKSAAAEGLD'
-    assert_equal(inverted_tryptic, lines[-1].chomp)
-    File.unlink(tmpfile) unless NODELETE
-  end
-
-  
-
-  ## HELPER ASSERTIONS:
-
-  def _are_inverted?(obj1, obj2) 
-    obj2_prots = obj2.prots
-    obj1.prots.each_with_index do |prot,i| 
-      if prot.aaseq.reverse != obj2_prots[i].aaseq
-        return false
-      end
-    end
-    return true
-  end
-
-  def _same_headers?(obj1, obj2)
-    obj1.prots.each_with_index do |prot,ind|
-      oprot = obj2.prots[ind]
-      if prot.header != oprot.header
-        return false
-      end
-    end
-    return true
-  end
-
-  # true if all prot AA seq's are the same
-  def _same_aaseqs?(obj1, obj2)
-    obj2_prots = obj2.prots
-    obj1.prots.each_with_index do |prot,i|
-      if prot.aaseq != obj2_prots[i].aaseq
-        return false
-      end
-    end
-    return true
-  end
-
-  # for two parallel fasta objects, determines if the list of proteins 
-  # are shuffled by examining the proteins and asking of > 4 are different
-  # returns true or false
-  def _are_shuffled?(obj1, obj2)
-    cnt = 0
-    obj1.prots.each_with_index do |prot,ind|
-      oprot = obj2.prots[ind]
-      if prot.header == oprot.header && prot.aaseq != oprot.aaseq
-        cnt += 1
-      end
-    end
-    if cnt > 4 
-      return true 
-    else
-      return false
-    end
-  end
-
-end
-
-=end

data/specs/gi_spec.rb

@@ -1,22 +0,0 @@
-require File.expand_path( File.dirname(__FILE__) + '/spec_helper'
 )
-require 'gi'
-
-
-describe GI, "given a 'GI' number" do
-  before(:all) do
-    @gi_num = 836805
-  end
-  it 'can query NCBI for annotation (fails nicely w/o connection)' do
-    annot = GI.gi2annot([@gi_num])
-    if annot
-      annot.first.should == 'proteosome component PRE4 [Saccharomyces cerevisiae]'
-    else
-      puts "- retrieval of gi failed gracefully w/o internet connection"
-    end
-end
-
-end
-
-
-
-

data/specs/load_bin_path.rb

@@ -1,7 +0,0 @@
-tmp = $VERBOSE ; $VERBOSE = nil
-LOAD_BIN_PATH = File.expand_path(File.dirname(__FILE__) + "#{File::SEPARATOR}..#{File::SEPARATOR}bin")
-$VERBOSE = tmp
-
-if ENV.key?("PATH")
-  ENV["PATH"] =  LOAD_BIN_PATH + File::PATH_SEPARATOR + ENV["PATH"]
-end

data/specs/merge_deep_spec.rb

@@ -1,13 +0,0 @@
-require File.expand_path( File.dirname(__FILE__) + '/spec_helper' )
-require 'merge_deep'
-
-describe 'merging one level deep' do
-  it 'works' do
-    base = {1=>"X", 3=>{6=>7, 8=>9}}
-    another = {1=>'y', 3=>{6=>9}}
-    ans = base.merge_deep(another, 1)
-    ans.should == {1=>'y', 3=>{6=>9, 8=>9}}
-  end
-end
-
-

data/specs/ms/gradient_program_spec.rb

@@ -1,77 +0,0 @@
-require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
-require 'ms/gradient_program'
-
-describe GradientProgram do
-  it 'can be set from a Thermo Xcal 2.X .meth file' do
-    data = [
-      [0.00, 95.0, 5.0, 0.0, 0.0, 38.0],
-      [1.00, 90.0, 10.0, 0.0, 0.0, 38.0],
-      [30.00, 85.0, 15.0, 0.0, 0.0, 38.0],
-      [40.00, 80.0, 20.0, 0.0, 0.0, 38.0],
-      [45.00, 78.0, 22.0, 0.0, 0.0, 38.0],
-      [50.00, 72.0, 28.0, 0.0, 0.0, 38.0],
-      [65.00, 60.0, 40.0, 0.0, 0.0, 38.0],
-      [72.00, 10.0, 90.0, 0.0, 0.0, 38.0],
-      [75.0, 10.0, 90.0, 0.0, 0.0, 38.0],
-      [81.00, 10.0, 90.0, 0.0, 0.0, 38.0],
-      [81.10, 95.0, 5.0, 0.0, 0.0, 38.0],
-      [90.00, 95.0, 5.0, 0.0, 0.0, 38.0],
-    ]
-
-    ms_pump_expected_tps = data.map do |ar| 
-      GradientProgram::TimePoint.new(ar[0], ar[-1], ar[1,4])
-    end
-    ms_pump_expected = GradientProgram.new('MS Pump', ms_pump_expected_tps, %w(A B C D))
-
-    data = [
-      [0.00, 0.0, 0.0, 100.0, 0.0, 40.0],
-      [90.0, 0.0, 0.0, 100.0, 0.0, 40.0],
-    ]
-    sample_pump_expected_tps = data.map {|ar| GradientProgram::TimePoint.new(ar[0], ar[-1], ar[1,4]) }
-    sample_pump_expected = GradientProgram.new('Sample Pump', sample_pump_expected_tps, %w(A B C D))
-
-    file = Tfiles + '/s01_anC1_ld020mM.meth'
-    File.open(file) do |fh|
-      gps = GradientProgram.all_from_handle(fh)
-      gps[0].should == ms_pump_expected
-      gps[1].should == sample_pump_expected
-    end
-  end
-
-  it 'can be set from a Thermo Xcal 1.X .RAW file (but missing pump_type)' do
-    file = Tfiles + '/opd1_020_beginning.RAW'
-    data = [[0.0, 0.0, 0.0, 100.0, 0.0, 200.0],
-      [1.0, 0.0, 0.0, 96.0, 4.0, 200.0],
-      [10.0, 0.0, 0.0, 96.0, 4.0, 200.0],
-      [11.0, 0.0, 0.0, 100.0, 0.0, 200.0],
-      [85.0, 0.0, 0.0, 100.0, 0.0, 200.0],]
-
-    time_points = data.map do |ar| 
-      GradientProgram::TimePoint.new(ar[0], ar[-1], ar[1,4])
-    end
-    pump_type = ''  ## need to get pump type...
-    ms_pump_expected = GradientProgram.new(pump_type, time_points, %w(A B C D))
-
-    data = [[0.0, 95.0, 5.0, 0.0, 0.0, 200.0],
-      [1.0, 95.0, 5.0, 0.0, 0.0, 200.0],
-      [61.0, 55.0, 45.0, 0.0, 0.0, 200.0],
-      [62.0, 5.0, 95.0, 0.0, 0.0, 200.0],
-      [67.0, 5.0, 95.0, 0.0, 0.0, 200.0],
-      [68.0, 95.0, 5.0, 0.0, 0.0, 200.0],
-      [85.0, 95.0, 5.0, 0.0, 0.0, 200.0],]
-    time_points = data.map do |ar| 
-      GradientProgram::TimePoint.new(ar[0], ar[-1], ar[1,4])
-    end
-    pump_type = ''  ## need to get pump type...
-    sample_pump_expected = GradientProgram.new(pump_type, time_points, %w(A B C D))
-
-    # we'd like to get an older .meth file to do this on
-    File.open(file) do |fh|
-      gps = GradientProgram.all_from_handle(fh)
-      gps[0].should == ms_pump_expected
-      gps[1].should == sample_pump_expected
-
-    end
-  end
-
-end