mspire 0.2.4 → 0.3.0

data/specs/spec_id/precision/prob_spec.rb

@@ -0,0 +1,111 @@
+require File.expand_path( File.dirname(__FILE__) + '/../../spec_helper' )
+
+require 'spec_id/precision/prob'
+require 'spec_id'
+require 'spec_id/proph'
+require 'validator'
+require 'fasta'
+require 'spec_id/sequest/params'
+
+
+describe 'finding precision Proph::Prot::Pep objects' do
+  before(:each) do
+    @spec_id = GenericSpecID.new
+    # actual sort order: 3, 0, 4, 1, 2
+    peps = [
+      # 0: canonical
+      {:peptide_sequence => '0', :initial_probability => 0.63, :nsp_adjusted_probability => 0.62, :weight => 1.0, :is_nondegenerate_evidence => true, :n_enzymatic_termini => 2, :n_sibling_peptides => 0.0, :n_instances => 1, :is_contributing_evidence => true}, 
+      # 1: lower init prob
+      {:peptide_sequence => '1', :initial_probability => 0.60, :nsp_adjusted_probability => 0.62, :weight => 1.0, :is_nondegenerate_evidence => true, :n_enzymatic_termini => 2, :n_sibling_peptides => 0.0, :n_instances => 1, :is_contributing_evidence => true}, 
+      # 2: lower nsp prob
+      {:peptide_sequence => '2', :initial_probability => 0.63, :nsp_adjusted_probability => 0.52, :weight => 1.0, :is_nondegenerate_evidence => true, :n_enzymatic_termini => 2, :n_sibling_peptides => 0.0, :n_instances => 1, :is_contributing_evidence => true}, 
+      # extra instances! (best hit)
+      {:peptide_sequence => '3', :initial_probability => 0.63, :nsp_adjusted_probability => 0.62, :weight => 1.0, :is_nondegenerate_evidence => true, :n_enzymatic_termini => 2, :n_sibling_peptides => 0.0, :n_instances => 5, :is_contributing_evidence => true}, 
+      # is nondegen = false 
+      {:peptide_sequence => '4', :initial_probability => 0.63, :nsp_adjusted_probability => 0.62, :weight => 1.0, :is_nondegenerate_evidence => false, :n_enzymatic_termini => 2, :n_sibling_peptides => 0.0, :n_instances => 1, :is_contributing_evidence => true},].map {|v| Proph::Prot::Pep.new(v) }
+      @spec_id.peps = peps
+  end
+
+  it 'runs without any validator' do
+    answer = SpecID::Precision::Prob.new.precision_vs_num_hits(@spec_id) 
+    answer.keys.map {|v| v.to_s }.sort.should == ["aaseqs", "charges", "count", "params", "pephits_precision", "probabilities"]
+    answer[:aaseqs].should == %w(3 0 4 1 2)
+  end
+
+  it 'returns modified peptides if any modified peptides' do
+    @spec_id.peps[1].mod_info = Sequest::PepXML::SearchHit::ModificationInfo.new(['MODIFIED', []])
+    answer = SpecID::Precision::Prob.new.precision_vs_num_hits(@spec_id) 
+    answer.keys.map {|v| v.to_s }.sort.should == ["aaseqs", "charges", "count", "modified_peptides", "params", "pephits_precision", "probabilities"]
+  end
+
+end
+
+
+=begin
+  it 'gets precision with all validators (including probability and decoy)' do
+    ## create some decoy peptides!
+    @spec_id.peps.sort_by {|pep| pep.probability }[100..-1].each_with_index do |pep,i|
+      if i % 3 == 0
+        pep.prots.each {|prot| prot.protein_name = 'DECOY_' + prot.protein_name }
+      end
+    end
+    # check which ones are ACTUALLY normal and decoy
+    (decoy, normal) = @spec_id.peps.partition do |pep|
+      pep.prots.all? {|prot| prot.protein_name =~ /^DECOY_/}
+    end
+    num_decoy = decoy.size
+    num_normal = normal.size
+  end
+
+prob_spec_helper = File.expand_path( File.dirname(__FILE__) + '/prob_spec_helper' )
+
+# this does a minimal test to see if this functions properly
+# (not for accuracy, which is done in validator_spec)
+## WITH FASTA FILE:
+base_dir = Tfiles_l + '/opd1_2runs_2mods/sequest'
+fasta_file = base_dir + '/ecoli_K12_ncbi_20060321.fasta'
+params_file = base_dir + '/ecoli.params'
+bias_file = base_dir + '/ecoli_K12_ncbi_20060321.bias.fasta'
+toppred_file = base_dir + '/ecoli_K12_ncbi_20060321.toppred.xml'
+
+fasta_file.should exist
+
+prob = Validator::Probability.new
+badaa_freq = Validator::AA.new('C', :frequency => 0.0115866200193321)
+badaa_dig = Validator::AA.new('C')
+bias = Validator::Bias.new(Fasta.new(bias_file))
+transmem = Validator::Transmem::Protein.new(toppred_file)
+decoy = Validator::Decoy.new(/^DECOY_/)
+
+turn_on_digestion = true
+if turn_on_digestion
+  # digestion based validators need this set!
+  digested_peps = Digestor.digest(Fasta.new(fasta_file), Sequest::Params.new(params_file))
+  [badaa_dig, bias, transmem].each do |val|
+    val.set_false_to_total_ratio(digested_peps)
+  end
+end
+transmem.transmem_status_hash = transmem.create_transmem_status_hash(@spec_id.peps)
+val_list = [decoy, badaa_freq, badaa_dig, prob, bias, transmem]
+
+opts = { :validators => val_list }
+
+
+hash = SpecID::Precision::Prob.new.precision_vs_num_hits(@spec_id, opts)
+#puts "OUTPUT: "
+#puts hash.to_yaml
+
+
+# frozen
+e_hash = ProbMSHelper::Answer2
+# hash[:pephits_precision].size.should == e_hash[:pephits_precision].size
+# other data types are tested above, just testing validators
+hash[:pephits_precision].zip( e_hash[:pephits_precision] ) do |val_hash, val_hash_e|
+  val_hash[:values].size.should == num_normal
+  #val_hash[:validator].should == val_hash_e[:validator]
+  val_hash[:values].zip(val_hash_e[:values]) {|v,e| v.should be_close(e, 0.000000001)}
+end
+    end
+end
+
+=end

data/specs/spec_id/proph/pep_summary_spec.rb

@@ -0,0 +1,143 @@
+require File.expand_path( File.dirname(__FILE__) + '/../../spec_helper' )
+
+require 'spec_id/proph/pep_summary'
+
+ToCheck = {
+  :spectrum_query => {:first => {:spectrum => "020.42.42.3", :start_scan=>42, :end_scan=>42, :precursor_neutral_mass=>1015.77285654469, :assumed_charge=>3, :index=>1 },
+    :last => {:spectrum=>"020.344.344.3", :start_scan=>344, :end_scan=>344, :precursor_neutral_mass=>1447.6040333025, :assumed_charge=>3, :index=>18 },
+},
+
+:search_hit => {:first => {:hit_rank=>1, :peptide=>"GTGVSVTR", :peptide_prev_aa=>"R", :peptide_next_aa=>"S", :protein=>"gi|49176370|ref|YP_026228.1|", :num_tot_proteins=>1, :num_matched_ions=>10, :tot_num_ions=>70, :calc_neutral_pep_mass=>1015.79382542, :massdiff=>-0.0209688753124055, :num_tol_term=>2, :num_missed_cleavages=>0, :is_rejected=>0, :xcorr=>1.06543827056885, :deltacn => 0.192325830459595, :deltacnstar=>0, :spscore=>77.8397979736328, :sprank=>3, :probability=>0.07881571, :fval=>0.1592, :ntt=>2, :nmc=> 0, :massd=>-0.021}, 
+  :last => { :hit_rank=>1, :peptide=>"VAALRVPGGASLTR", :peptide_prev_aa=>"R", :peptide_next_aa=>"K", :protein=>"gi|16129819|ref|NP_416380.1|", :num_tot_proteins=>1, :num_matched_ions=>16, :tot_num_ions=>78, :calc_neutral_pep_mass=>1447.58289842, :massdiff=> 0.0211348825000641, :num_tol_term=>2, :num_missed_cleavages=>1, :is_rejected=>0, :xcorr=>1.3090912103653, :deltacn => 0.259967535734177, :deltacnstar => 0, :spscore => 118.513412475586, :sprank => 4, :probability=>0.27738378, :fval=>1.3810, :ntt=>2, :nmc=>1, :massd=>0.021 },
+}
+}
+
+
+describe Proph::PepSummary, "reading a .xml file" do
+  before(:each) do
+    file = Tfiles + '/opd1_2runs_2mods/interact-opd1_mods__small.xml'
+    @obj = Proph::PepSummary.new(file)
+  end
+
+  it 'should raise an error if not a peptide prophet file' do
+    lambda { Proph::PepSummary.new(Tfiles + '/opd1/000.tpp_2.9.2.first10.xml')}.should raise_error(ArgumentError)
+  end
+
+  it 'has spectrum queries' do
+    @obj.spectrum_queries.size.should == 18
+
+    [:first, :last].each do |mth|
+      ToCheck[:spectrum_query][mth].each do |k,v|
+        @obj.spectrum_queries.send(mth).send(k).should == v
+      end
+      ToCheck[:search_hit][mth].each do |k,v|
+        @obj.spectrum_queries.send(mth).search_results.first.search_hits.first.send(k).should == v
+      end
+    end
+  end
+
+  it 'has pephits (which are descended from SearchHit)' do
+    @obj.peps.size.should == 18
+    [:hit_rank, :probability, :fval, :ntt, :nmc, :massd].each do |guy|
+      @obj.peps.first.should respond_to(guy)
+    end
+
+    [:first, :last].each do |mth|
+      ToCheck[:search_hit][mth].each do |k,v|
+        @obj.peps.send(mth).send(k).should == v
+      end
+    end
+
+  end
+
+end
+
+####################################################
+# OTHER TESTS NOT IMPLEMENTED (do we need these??)
+####################################################
+
+=begin
+
+require 'test/unit'
+require 'spec_id'
+require 'ms/scan'
+
+class ProphTest < Test::Unit::TestCase
+
+  def initialize(arg)
+    super(arg)
+    @tfiles = File.dirname(__FILE__) + '/tfiles/'
+    @pepproph_xml = @tfiles + 'pepproph_small.xml'
+  end
+
+  def Xtest_filter_by_min_pep_prob
+    obj = Proph::Pep::Parser.new
+    new_file = "tfiles/tmp.xml"
+    assert_match(/peptideprophet_result probability="0.[0-5]/, IO.read(@pepproph_xml))
+    obj.filter_by_min_pep_prob(@pepproph_xml, new_file, 0.50)
+    assert_no_match(/peptideprophet_result probability="0.[0-5]/, IO.read(new_file))
+    assert_match(/<peptideprophet_result[^>]*probability="0.[6-9][^>]*>/, IO.read(new_file))
+    File.unlink new_file
+  end
+
+  def Xtest_uniq_by_seqcharge
+    cls = Proph::Pep
+    p1 = cls.new({ :charge => '2', :sequence => 'PEPTIDE' })
+    p2 = cls.new({ :charge => '3', :sequence => 'PEPTIDE' })
+    p3 = cls.new({ :charge => '2', :sequence => 'PEPTIDE' })
+    p4 = cls.new({ :charge => '2', :sequence => 'APEPTIDE' })
+    p5 = cls.new({ :charge => '2', :sequence => 'APEPTIDE' })
+    un_peps = cls.uniq_by_seqcharge([p1,p2,p3,p4,p5])
+    ## WHY ISn't that working? below!
+    ##assert_equal([p1,p2,p4].to_set, un_peps.to_set)
+    assert(equal_sets([p1,p2,p4], un_peps))
+  end
+
+  def Xequal_sets(arr1, arr2)
+    c1 = arr1.dup
+    c2 = arr2.dup
+    arr1.each do |c|
+      arr2.each do |d|
+        if c == d
+          c1.delete c
+          c2.delete d
+        end
+      end
+    end
+    if (c1.size == c2.size) && (c1.size == 0)
+      true
+    else
+      false
+    end
+  end
+
+  def Xtest_arithmetic_avg_scan_by_parent_time
+    i1 = 100015.0
+    i2 = 30000.0
+    i3 = 100.0
+    t1 = 0.13
+    t2 = 0.23
+    t3 = 0.33
+    p1 = MS::Scan.new(1,1, t1)
+    p2 = MS::Scan.new(2,1, t2)
+    p3 = MS::Scan.new(3,1, t3)
+    s1 = MS::Scan.new(1,2,0.10, 300.2, i1, p1)
+    s2 = MS::Scan.new(2,2,0.20, 301.1, i2, p2)
+    s3 = MS::Scan.new(3,2,0.30, 302.0, i3, p3)
+    scan = Proph::Pep.new({:scans => [s1,s2,s3]}).arithmetic_avg_scan_by_parent_time
+    tot_inten = i1 + i2 + i3
+    tm = ( t1 * (i1/tot_inten) + t2 * (i2/tot_inten) + t3 * (i3/tot_inten) )
+    {:ms_level => 2, :prec_inten => 130115.0/3, :num => nil, :prec_mz => 301.1.to_f, :time => tm }.each do |k,v|
+      if k == :prec_mz  # not sure why this is bugging out, but..
+        assert_equal(v.to_s, scan.send(k).to_s)
+      else
+        assert_equal(v, scan.send(k))
+      end
+    end
+
+  end
+
+
+end
+
+=end

data/{test/tc_proph.rb → specs/spec_id/proph/prot_summary_spec.rb}

@@ -1,10 +1,51 @@
+require File.expand_path( File.dirname(__FILE__) + '/../../spec_helper' )
 
+require 'spec_id/proph/prot_summary'
 
-require 'test/unit'
-require 'spec_id'
-require 'spec/scan'
+describe Proph::ProtSummary, "reading a -prot.xml file" do
+  before(:each) do
+    file = Tfiles + '/opd1/000_020_3prots-prot.xml'
+    @obj = Proph::ProtSummary.new(file)
+  end
+
+  it 'extracts protein groups with probabilities' do
+    @obj.prot_groups.size.should == 3
+    @obj.prot_groups.first.probability.should == 1.0
+    @obj.prot_groups[2].probability == 0.98
+  end
+
+  it 'extracts protein hit attributes' do
+    prot = @obj.prot_groups[1].prots.first
+    %w(protein_name n_indistinguishable_proteins probability percent_coverage unique_stripped_peptides group_sibling_id total_number_peptides pct_spectrum_ids).zip(["gi|16132019|ref|NP_418618.1|", 1, 1.0, 13.0, "FRDGLK+AIQFAQDVGIRVIQLAGYDVYYQEANNETRR".split('+'), "a", 2, 0.41]) do |name, val|
+      prot.send(name).should == val
+    end
+  end
+
+  it 'can detect -prot.xml version' do
+    answer = ['1.9', '4']
+    files = ['/yeast_gly_small-prot.xml', '/interact-opd1_mods_small-prot.xml'].map {|v| Tfiles + v}
+    files.zip(answer) do |file,answ|
+      Proph::ProtSummary.new.get_version(file).should == answ 
+    end
+  end
+
+  it 'has prots, peps, and prot_groups ' do
+    @obj.peps.should_not be_nil
+    @obj.prots.should_not be_nil
+    @obj.prot_groups.should_not be_nil
+  end
 
+end
+
+####################################################
+# OTHER TESTS NOT IMPLEMENTED (do we need these??)
+####################################################
 
+=begin
+
+require 'test/unit'
+require 'spec_id'
+require 'ms/scan'
 
 class ProphTest < Test::Unit::TestCase
 
@@ -14,29 +55,6 @@ class ProphTest < Test::Unit::TestCase
     @pepproph_xml = @tfiles + 'pepproph_small.xml'
   end
 
-  def test_parse_protxml_file
-    file = @tfiles + 'opd1/000_020_3prots-prot.xml'
-    #obj = Proph::ProtSummary.new
-    obj = Proph::ProtSummary.new(file)
-    assert_equal(3, obj.prot_groups.size)
-    assert_equal("1.00", obj.prot_groups.first.probability)
-    assert_equal("0.98", obj.prot_groups[2].probability)
-    assert_equal_xml_atts_to_obj('protein_name="gi|16132019|ref|NP_418618.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="13.0" unique_stripped_peptides="FRDGLK+AIQFAQDVGIRVIQLAGYDVYYQEANNETRR" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="0.41"', obj.prot_groups[1].prots.first) 
-  end
-
-  def assert_equal_xml_atts_to_obj(string, obj, msg=nil)
-    parts = string.split(/\s+/)
-    parts.each do |part|
-      pi = part.split('=')
-      value = pi[1].sub(/^"/,'').sub(/"$/,'')
-      if pi[0] == "probability"
-        value = value.to_f
-      end
-      assert_equal(value, obj.send(pi[0].to_sym))
-    end
-  end
-
-
   def Xtest_filter_by_min_pep_prob
     obj = Proph::Pep::Parser.new
     new_file = "tfiles/tmp.xml"
@@ -85,12 +103,12 @@ class ProphTest < Test::Unit::TestCase
     t1 = 0.13
     t2 = 0.23
     t3 = 0.33
-    p1 = Spec::Scan.new(1,1, t1)
-    p2 = Spec::Scan.new(2,1, t2)
-    p3 = Spec::Scan.new(3,1, t3)
-    s1 = Spec::Scan.new(1,2,0.10, 300.2, i1, p1)
-    s2 = Spec::Scan.new(2,2,0.20, 301.1, i2, p2)
-    s3 = Spec::Scan.new(3,2,0.30, 302.0, i3, p3)
+    p1 = MS::Scan.new(1,1, t1)
+    p2 = MS::Scan.new(2,1, t2)
+    p3 = MS::Scan.new(3,1, t3)
+    s1 = MS::Scan.new(1,2,0.10, 300.2, i1, p1)
+    s2 = MS::Scan.new(2,2,0.20, 301.1, i2, p2)
+    s3 = MS::Scan.new(3,2,0.30, 302.0, i3, p3)
     scan = Proph::Pep.new({:scans => [s1,s2,s3]}).arithmetic_avg_scan_by_parent_time
     tot_inten = i1 + i2 + i3
     tm = ( t1 * (i1/tot_inten) + t2 * (i2/tot_inten) + t3 * (i3/tot_inten) )
@@ -106,3 +124,5 @@ class ProphTest < Test::Unit::TestCase
 
 
 end
+
+=end

data/{test/tc_protein_summary.rb → specs/spec_id/protein_summary_spec.rb}

@@ -1,3 +1,87 @@
+require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
+require 'spec_id/protein_summary'
+
+xdescribe ProteinSummary do
+
+  before(:all) do
+    @tf_proph = Tfiles_l + "/opd1/000_020-prot.xml"
+    @tf_summary = Tfiles_l + "/opd1/000_020-prot.summary.html"
+    @tf_bioworks_small = Tfiles + '/bioworks_small.xml'
+    @tf_bioworks_small_summary_html = Tfiles + '/bioworks_small.summary.html'
+    @tf_proph_cat_inv =  Tfiles + '/opd1/opd1_cat_inv_small-prot.xml'
+    @tf_proph_cat_inv_summary_html = Tfiles + '/opd1/opd1_cat_inv_small-prot.summary.html'
+    @tf_proph_cat_inv_summary_png = Tfiles + '/opd1/opd1_cat_inv_small-prot.summary.png'
+    @tf_peptide_count = Tfiles + "/peptide_counts.tmp.txt"
+    @no_delete = false
+  end
+
+  spec_large do
+    it 'does basic summary on prophet file' do
+      runit "-c 5.0 #{@tf_proph}"
+      @tf_summary.should exist
+      string = IO.read(@tf_summary)
+      string.should =~ /gi\|16132176\|ref\|NP_418775\.1\|/
+      string.should =~ /16132176/
+      File.unlink(@tf_summary) unless @no_delete
+    end
+  end
+
+  it 'does basic summary on bioworks.xml file' do
+    runit "#{@tf_bioworks_small}"
+    @tf_bioworks_small_summary_html.should exist
+    File.unlink @tf_bioworks_small_summary_html unless @no_delete
+    # @TODO: need to freeze the output here
+  end
+
+
+  it 'calculates precision values with bioworks files' do
+    ## Could reimplement a separate file approach?
+    #reply = `#{@cmd} -f #{@tf_bioworks_small} #{@tf_bioworks_small} --precision`
+    runit "#{@tf_bioworks_small} --precision"
+    IO.read(@tf_bioworks_small_summary_html).should =~ /# hits.*106/m
+    # should add more tests here...
+    @tf_bioworks_small_summary_html.should exist
+    File.unlink @tf_bioworks_small_summary_html unless @no_delete
+  end
+
+  it 'calculates precision values with prophet files' do
+    runit "#{@tf_proph_cat_inv} -f INV_ --prefix --precision"
+    html =  IO.read(@tf_proph_cat_inv_summary_html)
+    html.should =~ /# hits/
+    html.should =~ /2.*0\.0000/m
+    html.should =~ /3.*0\.3333/m
+    html.should =~ /7.*0\.5714/m
+
+    File.unlink @tf_proph_cat_inv_summary_html unless @no_delete
+    File.unlink @tf_proph_cat_inv_summary_png unless @no_delete
+  end
+
+  spec_large do
+    it 'gives correct peptide counts' do
+      runit "-c 5.0 #{@tf_proph} --peptide_count #{@tf_peptide_count}"
+      @tf_peptide_count.should exist
+      file = IO.read(@tf_peptide_count)
+      file.should include("gi|16132176|ref|NP_418775.1|\t2")
+      file.should include("gi|16131996|ref|NP_418595.1|\t1")
+      file.should include("gi|16131692|ref|NP_418288.1|\t4")
+      File.unlink @tf_peptide_count unless @no_delete
+    end
+  end
+
+  def runit(string_or_args)
+    args = if string_or_args.is_a? String
+             string_or_args.split(/\s+/)
+           else
+             string_or_args
+           end
+    ProteinSummary.new.create_from_command_line_args(args) 
+  end
+
+
+  end
+
+
+=begin
 
 require 'test/unit'
 require 'spec_id/protein_summary'
@@ -102,3 +186,4 @@ class ProphProtSummaryTest < Test::Unit::TestCase
 
 end
 
+=end

data/specs/spec_id/sequest/params_spec.rb

@@ -0,0 +1,68 @@
+require File.expand_path( File.dirname(__FILE__) + '/../../spec_helper' )
+require 'spec_id/sequest/params'
+
+
+describe "a sequest params object", :shared => true do
+  before(:each) do
+    @obj = Sequest::Params.new(@file)
+  end
+  it 'gives enzyme_specificity' do
+    ar = @obj.enzyme_specificity
+    ar.size.should == 3
+    ar.should == @enzyme_specificity
+  end
+  it 'returns static mods callable by key' do
+    @obj.add_Cterm_peptide.should == @add_Cterm_peptide
+  end
+end
+
+
+describe Sequest::Params, "with a bioworks 3.1 params" do
+  before(:all) do
+    @file = Tfiles + '/bioworks31.params'
+    @obj = Sequest::Params.new(@file)
+    @enzyme_specificity = [1, 'KR', '']
+    @add_Cterm_peptide = '0.0000'
+  end
+  it_should_behave_like 'a sequest params object'
+end
+
+describe Sequest::Params, "with a bioworks 3.2 params" do
+  before(:all) do
+    @file = Tfiles + '/bioworks32.params'
+    @obj = Sequest::Params.new(@file)
+    @enzyme_specificity = [1, 'KR', 'P']
+    @add_Cterm_peptide = '0.0000'
+  end
+  it_should_behave_like 'a sequest params object'
+end
+
+describe Sequest::Params, "with a bioworks 3.3 params" do
+  before(:all) do
+    @file = Tfiles + '/bioworks33.params'
+    @obj = Sequest::Params.new(@file)
+    @enzyme_specificity = [1, 'KR', '']
+    @add_Cterm_peptide = '0.0000'
+  end
+  it_should_behave_like 'a sequest params object'
+end
+
+describe Sequest::Params, "given a bioworks 3.2 params (from .srf file)" do
+  before(:all) do
+    @file = Tfiles + '/7MIX_STD_110802_1.sequest_params_fragment.srf'
+    @obj = Sequest::Params.new(@file)
+    @enzyme_specificity = [1, 'KR', 'P']
+    @add_Cterm_peptide = '0.0000'
+  end
+  it_should_behave_like 'a sequest params object'
+end
+
+
+describe Sequest::Params do
+  it '(private) can give a system independent basename' do
+    Sequest::Params.new._sys_ind_basename("C:\\Xcalibur\\database\\hello.fasta").should == "hello.fasta"
+    Sequest::Params.new._sys_ind_basename("/work/john/hello.fasta").should == "hello.fasta"
+  end
+  
+end
+