mspire 0.4.9 → 0.5.0

data/script/tpp_installer.rb

@@ -1,249 +0,0 @@
-#!/usr/bin/ruby -w
-
-###########################################################
-# GLOBAL CONFIG:
-
-## SYSTEM SPECIFIC VARIABLES:
-BIN_DIR = '/usr/bin/'
-NICE_PATH = '/usr/bin/nice' # path to nice program on your system
-
-## APACHE VARIABLES:
-MODS_AVAILABLE = '/etc/apache2/mods-available/include.load'
-MODS_ENABLED = '/etc/apache2/mods-enabled/include.load'
-# A File that will be included by the webserver to add specific directives:
-TPP_CONF = '/etc/apache2/conf.d/tpp.conf'
-# The system call to restart your apache
-RESTART_APACHE = '/etc/init.d/apache2 restart'
-
-## SETUP YOUR TPP INSTALL:
-TPP_INSTALL = "/work/tpp"   # directory to hold TPP executables, etc.
-# (where TPP_ROOT will actually go)
-TPP_DATA_PATH = "/work/tpp-data" # directory to hold your tpp data files
-
-TPP_WEB = '/tpp/'
-TPP_ISB_DEF_DIR = '/tools/bin/TPP/'
-TPP_ISB_DIR = 'tpp' # DON'T change this
-
-WEBSERVER_ROOT = '/var/www'
-TPP_WEB_PATH_STUB = WEBSERVER_ROOT # real directory to make soft link inside
-# For security reasons, TPP_VIS_PATH should NOT be the same as TPP_DATA_PATH
-TPP_VIS_PATH = WEBSERVER_ROOT + '/tpp-vis/'
-TPP_DATA_PATH_SOFT_LINK = WEBSERVER_ROOT + '/tpp'
-#TPP_WEB_PATH = WEBSERVER_ROOT + TPP_DATA_PATH_SOFT_LINK
-
-## VARIABLES YOU PROBABLY DON'T WANT TO CHANGE:
-XINTERACT_WRAPPER = 'xinteract'
-XINTERACT_ISB = 'xinteract-isb'
-makefile_incl = 'src/Makefile.incl'
-sequest2xml = 'src/Parsers/Algorithm2XML/Sequest2XML/Sequest2XML.cxx'
-
-### VARIABLES YOU PROBABLY SHOULDN'T CHANGE UNLESS YOU MODIFY the config
-### scripts
-HARD_CODED_TPP_INSTALL = '/tools/bin/TPP/tpp/'
-TPP_ROOT = HARD_CODED_TPP_INSTALL
-HARD_CODED_TPP_INSTALL_STUB = '/tools/bin/TPP' # real dir to hold soft link 
-###########################################################
-
-require 'fileutils'
-
-#######################################################
-# SUBROUTINES:
-#######################################################
-
-
-# creates the file with the given contents unless the file already exists AND already contains the contents
-def make_file(file, string)
-  puts "Trying to make file: #{file}"
-  if File.exist?(file) && string == IO.read(file) 
-    puts "File already exists with the given string" 
-  else
-    puts "Made file with given string"
-    File.open(file, "w") { |out| out.print string }
-  end
-end
-
-def mkpath(mpath)
-  path = mpath.chomp('/')
-  if File.exist? path; puts "Dir #{path} exists"
-  else 
-    FileUtils.mkpath path
-    puts "CREATING #{path}"
-  end
-end
-
-def chmod(code, path)
-  printf("Changing mode of #{path} to %o", code)
-  FileUtils.chmod code, path 
-end
-
-# creates wrapper around xinteract that runs #{XINTERACT_ISB} and moves files
-# to #{TPP_VIS_PATH}
-def xinteract_wrapper
-  tpp_data_path_wts = TPP_DATA_PATH.chomp('/')+'/'
-  "# Runs xinteract with whatever command lines given
-  # And then moves shtml files to #{TPP_VIS_PATH}
-  #{XINTERACT_ISB} $@
-  ruby -e 'if Dir[\"#{tpp_data_path_wts}*.shtml\"].size > 0 ; system \"mv #{tpp_data_path_wts}*.shtml #{TPP_VIS_PATH}\"; puts \"moving #{tpp_data_path_wts}*.shtml to #{TPP_VIS_PATH} for webserver security.\" end' 
-  ".gsub(/^\s+/,'')
-end
-
-def swap_line(file, regex, newval)
-  puts "EDITING: #{file}"
-  tmpfile = "tmp.tmp"
-  File.open(tmpfile, "w") do |out|
-    out.puts IO.readlines(file).collect{|line| line.sub(regex, newval) }
-  end
-  File.rename(tmpfile, file)
-end
-#{tpp_data_path_wts}*.shtml
-def soft_link(mtarget, mlink)
-  (link,target) = [mlink,mtarget].collect {|t| t.chomp('/')} 
-  if File.exist? link ;#{tpp_data_path_wts}*.shtml puts "Link #{link} exists!"
-  else
-    FileUtils.ln_sf target, link
-    puts "CREATING soft link: #{link} -> #{target}"
-  end
-end
-
-def sys(string)
-  puts "PERFORMING: #{string}"
-  puts `#{string}`
-end
-
-def modify_and_restart_apache(tpp_root, webserver_root, tpp_vis_path, mods_avail, mods_enab)
-  # APACHE:
-  soft_link(mods_avail, mods_enab)
-
-  conf_string = <<END_DOC
-#
-# ISB-Tools Trans Proteomic Pipeline directive
-#
-
-Alias /tpp/html \"#{tpp_root}html\"
-<Directory \"#{tpp_root}html\">
-    AllowOverride None
-    Options Includes Indexes FollowSymLinks MultiViews
-    Order allow,deny
-    Allow from all
-</Directory>
-
-<Directory \"#{tpp_root}schema\">
-    AllowOverride None
-    Options Includes Indexes FollowSymLinks MultiViews
-    Order allow,deny
-    Allow from all
-</Directory>
-
-ScriptAlias /tpp/cgi-bin/ \"#{tpp_root}cgi-bin/\"
-<Directory \"#{tpp_root}cgi-bin\">
-    AllowOverride AuthConfig Limit
-    Options ExecCGI
-    Order allow,deny
-    Allow from all
-    SetEnv WEBSERVER_ROOT #{webserver_root}
-</Directory>
-
-<Directory \"#{tpp_vis_path}\">
-  Options Includes
-</Directory>
-
-END_DOC
-
-  make_file(TPP_CONF, conf_string)
-  sys "#{RESTART_APACHE}"
-end
-
-
-
-###############################################################
-# MAIN
-###############################################################
-
-if ARGV.size < 1
-  puts "
-  usage: #{File.basename(__FILE__)} trans_proteomic_pipeline_dir
-
-  Will install tpp on a ubuntu system (perhaps a debian system, too?).  With
-  slight modifications, you may get this to install on other machines.
-  Requires apache2 (sudo apt-get apache2).  The installation uses all the
-  default TPP locations because a lot of these are quite hard-coded in the tpp
-  despite the config files they use.  Instead, soft-links are made so that you
-  can configure your system however you desire. Will probably not clobber
-  existing files, but it might ;)
-
-  PLEASE SET GLOBAL VARIABLES in this script (#{File.basename(__FILE__)})!
-
-  PREREQS:
-  sudo apt-get install <prereq>
-    make, g++, ruby, apache2, libzzip-dev, libgd2-dev, libpng3-dev libexpat-dev 
-  --> or all on one line:
-  sudo apt-get install make g++ ruby apache2 libzzip-dev libgd2-dev libpng3-dev libexpat-dev
-
-  In all likelihood, this will need to be run as root.
-  "
-  exit
-end
-
-#########################
-# MAKE INSTALLATION DIR:
-#########################
-mkpath HARD_CODED_TPP_INSTALL_STUB  # dir to hold soft link
-mkpath TPP_INSTALL
-soft_link(TPP_INSTALL, HARD_CODED_TPP_INSTALL.sub(/\/$/,''))
-
-############################
-# MAKE WEB DIRS:
-############################
-mkpath TPP_WEB_PATH_STUB
-soft_link(TPP_DATA_PATH, TPP_DATA_PATH_SOFT_LINK)
-
-mkpath TPP_DATA_PATH.chomp('/')
-chmod(0777, TPP_DATA_PATH.chomp('/'))
-mkpath TPP_VIS_PATH.chomp('/')
-
-## VERY SPECIFIC to OUR SYSTEM
-soft_link('/project/marcotte/marcotte/ms', TPP_DATA_PATH.chomp('/') + '/ms')
-system "sudo chown john:marcotte #{TPP_DATA_PATH.chomp('/')}"
-system "sudo chown john:marcotte #{TPP_VIS_PATH.chomp('/')}"
-
-############################
-# FIX UP APACHE
-############################
-modify_and_restart_apache(TPP_ROOT, WEBSERVER_ROOT, TPP_VIS_PATH,  MODS_AVAILABLE, MODS_ENABLED)
-
-############################
-# MAKE and INSTALL
-############################
-Dir.chdir ARGV[0] do
-  ############################
-  # SWAP OUT BAD LINES
-  ############################
-  swap_line(makefile_incl, /TPP_ROOT=.*/, 'TPP_ROOT='+TPP_ROOT)
-  swap_line(makefile_incl, /TPP_WEB=.*/, 'TPP_WEB='+TPP_WEB)
-  swap_line(sequest2xml, /if\(k < 12\) \{/, 'if(k < 6) {' )
-  swap_line(sequest2xml, /cerr << " error: length of " << result->spectrum_ << " less than 13" << endl;/, 'cerr << " error: length of " << result->spectrum_ << " less than 6" << endl;')
-  # CLEAN, MAKE, MAKE INSTALL:
-  Dir.chdir('src') do
-    sys "make clean"
-    sys "make all"
-    sys "make install"
-  end
-end
-
-############################
-# CREATE ADDITIONAL LINKS:
-############################
-soft_link(NICE_PATH, '/bin/nice')
-soft_link(TPP_ROOT + 'bin/xinteract', BIN_DIR + XINTERACT_ISB)
-puts "LINKING batchcoverage to #{BIN_DIR}batchcoverage"
-soft_link(TPP_ROOT + 'bin/batchcoverage', BIN_DIR + 'batchcoverage')
-soft_link(TPP_ROOT + 'bin/Sequest2XML', BIN_DIR + 'Sequest2XML')
-
-############################
-# CREATE xinteract wrapper:
-############################
-puts "CREATING xinteract wrapper script '#{BIN_DIR}#{XINTERACT_WRAPPER}'"
-File.open("#{BIN_DIR}#{XINTERACT_WRAPPER}", "w") do |fh| fh.print(xinteract_wrapper) end
-puts `chmod +x #{BIN_DIR}#{XINTERACT_WRAPPER}`
-
-

data/specs/align_spec.rb

@@ -1,79 +0,0 @@
-require File.expand_path( File.dirname(__FILE__) + '/spec_helper' )
-
-require 'align'
-
-describe Align do
-
-  before(:each) do
-    @mz1 = Tfiles + '4-03-03_mzXML/000.mzXML.timeIndex'
-    @mz2 = Tfiles + '4-03-03_mzXML/020.mzXML.timeIndex'
-    @prt = Tfiles + '4-03-03_small-prot.xml'
-    @pep = Tfiles + '4-03-03_small.xml'
-  end
-
-  it_should 'finds overlapping peptides of same seq+charge' do
-    s1 = 'DETTIVEGAGDAEAIQGR'
-    c1 = '2'
-    s2 = 'TDDVAGDGTTTATVLAQALVR'
-    c2 = '2'
-
-    al = Align.new
-    pep1 = al.peps_with_scans([@mz1], @prt, @pep, 0.05 ,0.05 ,0.05  )
-    pep2 = al.peps_with_scans(@mz2, @prt, @pep,  0.98,0.98,0.98 )
-    olap = al.overlapping_peps_by_seqcharge([pep1, pep2])
-    olap.each do |peps|
-      has_seqcharges = []
-      peps.each do |pep|
-        if pep.sequence == s1 && pep.charge == c1
-          has_seqcharges << true
-        elsif pep.sequence == s2 && pep.charge == c2
-          has_seqcharges << true
-        else
-          has_seqcharges << false
-        end
-      end
-      has_seqcharges.each { |c| c.should be_true }
-    end
-  end
-
-  ### !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-  # @TODO: CURRENT WORK!
-  it_should 'should find overlapping peptides at a seqcharge with a filter' do
-    al = Align.new
-    pep1 = al.peps_with_scans([@mz1], @prt, @pep, 0.0 ,0.0 ,0.0  )
-    pep2 = al.peps_with_scans(@mz2, @prt, @pep, 0.0, 0.0, 0.0 )
-    max_dups = nil
-    outlier_cutoff = 0.0
-    olap = al.overlapping_peps_by_seqcharge_with_filter([pep1, pep2], max_dups, outlier_cutoff)
-    olap.each do |peps|
-      p peps
-    end
-  end
-
-  it_should 'should toss outliers' do
-
-    # Consistency/sanity checks right now (not accuracy)
-    x = [-10,-9,-8,-7,-6,-5,-4,-3,-2,-1,10,0 ,1,2,3,4,5,6,7,8,9]
-    y = [-10,-9,-8,-7,-6,-5,-4,-3,-2,-1,0 ,10,1,2,3,4,5,6,7,8,9]
-    expx2 = [-10,-9,-8,-7,-6,-5,-4,-3,-2,-1,1,2,3,4,5,6,7,8,9]
-    expy2 = [-10,-9,-8,-7,-6,-5,-4,-3,-2,-1,1,2,3,4,5,6,7,8,9]
-
-    pcls = Proph::Pep
-    scls = MS::Scan
-
-    pep_groups = [x,y].collect do |arr|
-      arr.collect do |val| 
-        pep = pcls.new
-        pep.arithmetic_avg_scan_by_parent_time = scls.new(nil,nil,val.to_f)
-        pep
-      end
-    end
-
-    al = Align.new 
-    deviations = 3.2
-    size_before = pep_groups.first.size
-    al.toss_outliers(pep_groups, deviations)
-    (size_before - pep_groups.first.size).should == 2
-  end
-
-end

data/specs/bin/bioworks_to_pepxml_spec.rb

@@ -1,79 +0,0 @@
-require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
-require 'fileutils'
-
-
-$XML_SANITY_LINES = ['<sample_enzyme name="Trypsin">', '<specificity cut="KR" no_cut="P" sense="C"/>', '<parameter name="diff_search_options" value="0.000000 S 0.000000 C 0.000000 M 0.000000 X 0.000000 T 0.000000 Y"/>']
-
-$XML_SANITY_MATCHES = [/<spectrum_query spectrum="0\d0.\d+.\d+.[123]" start_scan="\d+" end_scan="\d+" precursor_neutral_mass="[\d\.]+" assumed_charge="[123]" index="\d+">/,
-  /	<search_hit hit_rank="\d" peptide="[\w\-\.]+" peptide_prev_aa="." peptide_next_aa="." protein=".*" num_tot_proteins="\d+" num_matched_ions="\d+" tot_num_ions="\d+" calc_neutral_pep_mass="[\d\.]+" massdiff="[\+\-][\d\.]+" num_tol_term="\d" num_missed_cleavages="\d" is_rejected="[01]">/, 
-  /<search_score name="xcorr" value="[\d\.]+"\/>/,
-  /<search_score name="deltacn" value="[\d\.]+"\/>/, 
-  /<search_score name="deltacnstar" value="[01]"\/>/, 
-  /<search_score name="spscore" value="[\d\.]+"\/>/, 
-  /<search_score name="sprank" value="\d+"\/>/,
-]
-
-
-describe 'bioworks_to_pepxml.rb' do
-  before(:all) do
-    @tf_mzxml_path = Tfiles_l + "/yeast_gly_mzXML"
-    @tf_bioworks_xml = Tfiles + "/bioworks_small.xml"
-    @tf_params = Tfiles + '/bioworks32.params'
-    @out_path = Tfiles + '/pepxml/'
-    @progname = 'bioworks_to_pepxml.rb'
-    @no_delete = false
-  end
-
-  it_should_behave_like "a cmdline program"
-
-  def _basic(cmd, prc)
-    puts "Performing: #{cmd}" if $DEBUG
-    reply = `#{cmd}`
-    puts reply if $DEBUG
-    %w(000 020).each do |file|
-      ffile = @out_path + file + ".xml"
-      prc.call(ffile)
-    end
-  end
-
-  spec_large do
-    it 'works on a real bioworks.xml file' do
-      cmd = "#{@cmd} -p #{@tf_params} -o #{@out_path} #{@tf_bioworks_xml} -m #{@tf_mzxml_path} -d /work/special/path --copy_mzxml"
-      ## FILES EXIST:
-      prc = proc {|file| 
-        file.exist_as_a_file?.should be_true
-        beginning = IO.readlines(file)[0,50].join("\n")
-        $XML_SANITY_LINES.each do |line|
-          beginning.should include(line)
-          #beginning.include?(line).should be_true
-        end
-        $XML_SANITY_MATCHES.each do |match|
-          beginning.should =~ match
-        end
-      }
-      _basic(cmd, prc)
-      ## COPY MZXML:
-      %w(000 020).each do |file|
-        mzxml_file = File.join(@out_path, "#{file}.mzXML")
-        mzxml_file.exist_as_a_file?.should be_true
-      end
-      ## CLEANUP:
-      unless @no_delete then FileUtils.rm_rf(@out_path) end
-    end
-  end
-
-  spec_large do
-    it 'transforms database name when its proper to do so' do
-      cmd = "#{@cmd} -p #{@tf_params} -o #{@out_path} #{@tf_bioworks_xml} -m #{@tf_mzxml_path}" 
-      db_re = /C:\\Xcalibur\\database\\ecoli_K12_ncbi_20060321.fasta/
-      IO.read(@tf_params).should =~ db_re
-      prc = proc {|file|
-        file.exist_as_a_file?.should be_true
-        IO.read(file).should_not =~ db_re
-      }
-      _basic(cmd, prc)
-      unless @no_delete then FileUtils.rm_rf(@out_path) end
-    end
-  end
-end
-

data/specs/bin/fasta_shaker_spec.rb

@@ -1,259 +0,0 @@
-require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
-
-require 'fasta'
-
-
-class Fasta
-  def same_sized_proteins?(other_fasta_obj_or_file)
-    other = Fasta.to_fasta(other_fasta_obj_or_file)
-    @prots.zip(other.prots).all? do |a,b|
-      a.aaseq.size == b.aaseq.size
-    end
-  end
-
-  # This is tough to say 'for sure'  Right now, we consider the proteins
-  # shuffled if they are all the same size and 2/3 or more of the peptides are
-  # different than the other (this is designed for small sets of proteins
-  # where it is possible one of the peptides is equal to the other).
-  def shuffled?(other_fasta_obj_or_file)
-    other = Fasta.to_fasta(other_fasta_obj_or_file)
-    if !same_sized_proteins?(other)
-      false
-    else
-      (same, different) = @prots.zip(other.prots).partition do |prota, protb|
-        prota == protb
-      end
-      fraction_different = different.size.to_f / (same.size + different.size)
-      fraction_different >= 2.0/3
-    end
-  end
-end
-
-describe "a manipulator of a fasta file", :shared => true do
-  before(:all) do
-    @filestring = ">gi|P1
-AMKRGAN
->gi|P2
-CRGATKKTAGRPMEK
->gi|P3
-PEPTIDE
-"
-
-    @rev_filestring = ">gi|P1
-NAGRKMA
->gi|P2
-KEMPRGATKKTAGRC
->gi|P3
-EDITPEP
-"
-
-    @rev_pref_filestring = ">REV_gi|P1
-NAGRKMA
->REV_gi|P2
-KEMPRGATKKTAGRC
->REV_gi|P3
-EDITPEP
-"
-
-    @rev_tryptic_filestring = ">gi|P1
-MAKRNAG
->gi|P2
-CRTAGKKEMPRGATK
->gi|P3
-EDITPEP
-"
-  end
-
-
-  before(:each) do
-    testdir = File.dirname(__FILE__)
-    @tmpfile = Tfiles + "/littlefasta.trash.fasta"
-    @f = Tfiles + "/trash.fasta"
-    File.open(@tmpfile, "w") {|fh| fh.print @filestring }
-  end
-
-  after(:each) do
-    File.unlink @tmpfile if File.exist? @tmpfile
-    File.unlink @f if File.exist? @f
-  end
-
-  it 'reverses protein sequences' do
-    reverse_the_file
-    fastap(@f).to_s.should == @rev_filestring
-  end
-
-  def reverse_the_file
-    do_it(:reverse)
-  end
-
-  it 'shuffles protein sequences' do
-    shuffle_the_file
-    Fasta.new(@f).shuffled?(Fasta.from_string(@filestring)).should be_true
-  end
-
-  def shuffle_the_file
-    do_it(:shuffle)
-  end
-
-  it 'concatenates sequences' do
-    concatenate_sequences
-    lns = fastalns(@f)
-    strlns(@filestring).should == lns[0..5] # first part equal
-    strlns(@rev_pref_filestring).should == lns[6..-1] # "second part equal")      
-  end
-
-  def concatenate_sequences
-    do_it(:reverse, :cat => true, :prefix => 'REV_')
-  end
-
-  it 'makes prefixes' do
-    make_prefixes
-    #@shaker.reverse(@tmpfile, :out => @f, :prefix => 'SILLY_')
-    fp = fastap(@f)
-    fp.each do |prt|
-      prt.header.should match(/^>SILLY_.+/)
-    end
-  end
-
-  def make_prefixes
-    do_it(:reverse, :prefix => 'SILLY_')
-  end
-
-  it 'makes fractions of proteins' do
-    make_fractions_of_proteins(1.0/3)
-    fastap(@f).size.should == 1
-    fastap(@f).first.header.should =~ /^>[^M]/
-
-    # this guy gets rounded up on the command line so that it fails there
-    #make_fractions_of_proteins(2.0/3)
-    #fastap(@f).size.should == 2
-    #fastap(@f).each do |prt|
-    #  prt.header.should =~ /^>[^M]/
-    #end
-
-    make_fractions_of_proteins(1.0)
-    fastap(@f).size.should == 3
-    fastap(@f).each do |prt|
-      prt.header.should =~ /^>[^M]/
-    end
-  end
-
-  def make_fractions_of_proteins(fraction)
-    do_it(:shuffle, :fraction => fraction)
-  end
-
- 
-  it 'makes fractions with labels (for > 1)' do
-    make_fractions_of_proteins(1.1)
-    fastap(@f).size.should == 4
-    fastap(@f).any? do |prt|
-      prt.header =~ /^>[^M]/
-    end.should be_true
-
-
-    make_fractions_of_proteins(2.6)
-    fastap(@f).size.should == 8
-
-    make_reverse_cat_fractions(2.0)
-    fastap(@f).size.should == 9
-
-    fp = Fasta.new(@f)
-    fp[0..2].each do |prt|
-      prt.header.should =~ /^>/
-    end
-    fp[3..5].each do |prt|
-      prt.header.should =~ /^>MINE_f0_/
-    end
-    fp[6..8].each do |prt|
-      prt.header.should =~ /^>MINE_f1_/
-    end
-  end
-
-  def make_reverse_cat_fractions(fraction, prefix='MINE_')
-    do_it(:reverse, :fraction => fraction, :cat => true, :prefix => prefix)
-  end
-
-  def reverse_tryptic_peptides
-    do_it(:reverse, :tryptic_peptides => true)
-  end
-
-    it 'reverses tryptic peptides' do
-      reverse_tryptic_peptides
-      Fasta.from_string(@rev_tryptic_filestring).should == Fasta.new(@f)
-    end
-
-  def shuffle_tryptic_peptides
-    do_it(:shuffle, :tryptic_peptides => true)
-  end
-
-  it 'shuffles tryptic peptides (rerun on failure to recheck)' do
-    shuffle_tryptic_peptides
-    lns = fastap(@f).to_s.split("\n")
-    lns[1][2..3].should == 'KR'
-    lns[3][1..1].should == 'R'
-    lns[3].size.should == 'CRGATKKTAGRPMEK'.size
-    lns[3].should_not == 'CRGATKKTAGRPMEK' #sequence is randomised from original [remote chance of failure] rerun to make sure
-  end
-
-    def strlns(str)
-      str.split("\n")
-    end
-
-  def fastalns(fn)
-    fn.exist_as_a_file?.should be_true
-    IO.read(fn).split("\n")
-  end
-
-  # returns the fasta object proteins
-  def fastap(fn)
-    @f.exist_as_a_file?.should be_true
-    Fasta.new(fn).prots
-  end
-
-end
-
-describe FastaShaker, "by method call" do
-
-  before(:all) do
-    @shaker = FastaShaker.new
-  end
-
-  it_should_behave_like "a manipulator of a fasta file"
-
-  def do_it(method, additional_opts={})
-    opts = {:out => @f}
-    @shaker.send(method, @tmpfile, opts.merge(additional_opts))  
-  end
-
-end
-
-
-describe FastaShaker, "by command line long args" do
-  before(:all) do
-    @progname = 'fasta_shaker.rb'
-  end
-
-  it_should_behave_like "a cmdline program"
-  it_should_behave_like "a manipulator of a fasta file"
-
-  # returns an array of the args
-  def opts_to_cmd_args(hash)
-    opts = []
-    hash.each do |k,v|
-      opts.push('--' + k.to_s)
-      unless (v == true) or (v == false)
-        opts.push(v)
-      end
-    end
-    opts
-  end
-  
-  def do_it(method, additional_opts={})
-    opts = {:out => @f}
-    opts.merge!(additional_opts)
-    cmd = [@cmd, method, @tmpfile, *(opts_to_cmd_args(opts))].join(" ")
-    #puts cmd
-    system cmd
-  end
-
-end