mspire 0.4.2 → 0.4.4
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.
- data/INSTALL +10 -3
- data/changelog.txt +17 -0
- data/lib/archive/targz.rb +94 -0
- data/lib/core_extensions.rb +16 -0
- data/lib/mspire.rb +1 -1
- data/lib/pi_zero.rb +227 -0
- data/lib/qvalue.rb +152 -0
- data/lib/spec_id/mass.rb +2 -1
- data/lib/spec_id/precision/filter.rb +11 -0
- data/lib/spec_id/precision/filter/cmdline.rb +1 -0
- data/lib/spec_id/precision/prob.rb +2 -3
- data/lib/spec_id/precision/prob/cmdline.rb +8 -2
- data/lib/spec_id/proph/pep_summary.rb +1 -1
- data/lib/spec_id/proph/prot_summary.rb +2 -2
- data/lib/spec_id/srf.rb +95 -11
- data/lib/validator/background.rb +4 -0
- data/lib/validator/cmdline.rb +41 -1
- data/lib/validator/probability.rb +3 -0
- data/specs/bin/prob_validate_spec.rb +13 -1
- data/specs/pi_zero_spec.rb +104 -0
- data/specs/qvalue_spec.rb +39 -0
- data/specs/validator/background_spec.rb +14 -0
- metadata +11 -3
data/INSTALL
CHANGED
@@ -2,14 +2,17 @@
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Prerequisites
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-------------
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-
Much of the package will work without any prerequisites at all. Some functionality may require addition ruby packages or other converters.
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Much of the package will work without any prerequisites at all. Some functionality may require addition ruby packages or other converters.
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* libjtp - generic library installed automatically if you install mspire with rubygems (or 'gem install libjtp')
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### XML parsing:
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* [xmlparser](http://www.yoshidam.net/Ruby.html) (comes with one-click Windows; on Ubuntu: 'sudo apt-get libxml-parser-ruby1.8')
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* [axml](http://axml.rubyforge.org/) dom wrapper for xmlparser. ('gem install axml')
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* ['t2x'](archive/t2x) linux executable to convert .RAW files (Xcalibur 1.x) to version 1 mzXML files
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Optional:
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### Optional:
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* ['t2x'](archive/t2x) linux executable to convert .RAW files (Xcalibur 1.x) to version 1 mzXML files
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* [libxml](http://libxml.rubyforge.org/) can use instead of xmlparser. In Ubuntu: sudo apt-get install libxml2 libxml2-dev ; sudo gem install libxml-ruby --remote
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* [gnuplot](http://rgplot.rubyforge.org/) ('gem install gnuplot'). For some plotting. Of course, you'll need [gnuplot](http://www.gnuplot.info/) before this package will work. Under one-click installer for windows this package requires a little configuration. It works with no configuration on cygwin (or linux).
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@@ -23,6 +26,9 @@ See [installation under cygwin](cygwin.html) if you're on Windows.
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Development
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-----------
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NOTE: If you are interested in becoming a developer on this project (i.e., write access to the repository) please [contact me](http://rubyforge.org/users/jtprince/)
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anonymous svn checkout:
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svn checkout svn://rubyforge.org/var/svn/mspire
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run tests with large files: rake spec SPEC_LARGE=t
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run test on one file: rake spec SPEC=specs/{path_to_spec_file}
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data/changelog.txt
CHANGED
@@ -191,3 +191,20 @@ evaluation))
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1. added MS::MSRun.open method
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2. added method to write dta files from SRF
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## version 0.4.3
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1. added to_mfg_file from SRF
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2. added to_dta_files from SRF complete with streaming .tar.gz output (and
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supporting .zip output but it has to make tmp files)
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## version 0.4.4
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1. implemented q-value and pi_0 methods of Storey
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2. can do complete q-value calculations given p-values
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3. can determine a pi_0 given a list of target and decoy values (as booleans)
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4. can determine a pi_0 given a list containing numbers of decoy and target
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values as is often encountered with filtering
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5. prob_validate.rb implements a q-value option for turning PeptideProphet
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probabilities into q-values
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6. filter_validate.rb implements a p value method using xcorr values, however,
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this is not very effective since xcorr values underrepresent the the
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difference between good hits and bad hits
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@@ -0,0 +1,94 @@
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require 'archive/tar/minitar'
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require 'stringio'
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module Archive::Tar::Minitar
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# entry may be a string (the name), or it may be a hash specifying the
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# following:
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# :name (REQUIRED)
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# :mode 33188 (rw-r--r--) for files, 16877 (rwxr-xr-x) for dirs
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# (0O100644) (0O40755)
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# :uid nil
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# :gid nil
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# :mtime Time.now
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#
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# if data == nil, then this is considered a directory!
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# (use an empty string for a normal empty file)
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# data should be something that can be opened by StringIO
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def self.pack_as_file(entry, data, outputter) #:yields action, name, stats:
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outputter = outputter.tar if outputter.kind_of?(Archive::Tar::Minitar::Output)
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stats = {}
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stats[:uid] = nil
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stats[:gid] = nil
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stats[:mtime] = Time.now
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if data.nil?
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# a directory
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stats[:size] = 4096 # is this OK???
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stats[:mode] = 16877 # rwxr-xr-x
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else
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stats[:size] = data.size
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stats[:mode] = 33188 # rw-r--r--
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end
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if entry.kind_of?(Hash)
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name = entry[:name]
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entry.each { |kk, vv| stats[kk] = vv unless vv.nil? }
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else
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name = entry
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end
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if data.nil? # a directory
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yield :dir, name, stats if block_given?
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outputter.mkdir(name, stats)
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else # a file
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outputter.add_file_simple(name, stats) do |os|
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stats[:current] = 0
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yield :file_start, name, stats if block_given?
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StringIO.open(data, "rb") do |ff|
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until ff.eof?
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stats[:currinc] = os.write(ff.read(4096))
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stats[:current] += stats[:currinc]
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yield :file_progress, name, stats if block_given?
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end
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end
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yield :file_done, name, stats if block_given?
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end
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end
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end
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end
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require 'zlib'
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file_names = ['wiley/dorky1', 'dorky2', 'an_empty_dir']
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file_data_strings = ['my data', 'my data also', nil]
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module Archive ; end
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# usage:
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# require 'archive/targz'
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# Archive::Targz.archive_as_files("myarchive.tgz", %w(file1 file2 dir),
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# ['data for file1', 'data for file2', nil])
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module Archive::Targz
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# requires an archive_name (e.g., myarchive.tgz) and parallel filename and
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# data arrays:
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# filenames = %w(file1 file2 empty_dir)
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# data_ar = ['stuff in file 1', 'stuff in file2', nil]
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# nil as an entry in the data_ar means that an empty directory will be
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# created
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def self.archive_as_files(archive_name, filenames=[], data_ar=[])
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tgz = Zlib::GzipWriter.new(File.open(archive_name, 'wb'))
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Archive::Tar::Minitar::Output.open(tgz) do |outp|
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filenames.zip(data_ar) do |name, data|
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Archive::Tar::Minitar.pack_as_file(name, data, outp)
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end
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end
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end
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end
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class Float
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# 3 following methods from http://www.hans-eric.com/code-samples/ruby-floating-point-round-off/
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def round_to(x)
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(self * 10**x).round.to_f / 10**x
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end
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def ceil_to(x)
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(self * 10**x).ceil.to_f / 10**x
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end
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def floor_to(x)
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(self * 10**x).floor.to_f / 10**x
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end
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end
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data/lib/mspire.rb
CHANGED
data/lib/pi_zero.rb
ADDED
@@ -0,0 +1,227 @@
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require 'rsruby'
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require 'gsl'
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require 'vec'
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require 'vec/r'
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require 'enumerator'
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module PiZero
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class << self
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# takes a sorted array of p-values (floats between 0 and 1 inclusive)
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# returns [thresholds_ar, instantaneous pi_0 calculations_ar]
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# evenly incremented values will be used by default:
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# :start=>0.0, :stop=>0.9, :step=>0.01
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def pi_zero_hats(sorted_pvals, args={})
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defaults = {:start => 0.0, :stop=>0.9, :step=>0.05 }
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margs = defaults.merge( args )
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(start, stop, step) = margs.values_at(:start, :stop, :step)
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# From Storey et al. PNAS 2003:
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lambdas = [] # lambda
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pi_zeros = [] # pi_0
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total = sorted_pvals.size # m
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# totally retarded implementation with correct logic:
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start.step(stop, step) do |lam|
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lambdas << lam
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(greater, less) = sorted_pvals.partition {|pval| pval > lam }
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pi_zeros.push( greater.size.to_f / ( total * (1.0 - lam) ) )
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end
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[lambdas, pi_zeros]
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end
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# expecting x and y to make a scatter plot descending to a plateau on the
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# right side (which is assumed to be of increasing noise as it goes to the
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# right)
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# returns the height of the plateau at the right edge
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#
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# *
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# *
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# *
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# **
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# ** *** * *
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# ***** **** ***
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def plateau_height(x, y)
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=begin
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require 'gsl'
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x_deltas = (0...(x.size-1)).to_a.map do |i|
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x[i+1] - x[i]
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end
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y_deltas = (0...(y.size-1)).to_a.map do |i|
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y[i+1] - y[i]
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end
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new_xs = x.dup
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new_ys = y.dup
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x_deltas.reverse.each do |delt|
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new_xs.push( new_xs.last + delt )
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end
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y_cnt = y.size
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y_deltas.reverse.each do |delt|
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y_cnt -= 1
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new_ys.push( y[y_cnt] - delt )
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end
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x_vec = GSL::Vector.alloc(new_xs)
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y_vec = GSL::Vector.alloc(new_ys)
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coef, cov, chisq, status = GSL::Poly.fit(x_vec,y_vec, 3)
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coef.eval(x.last)
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#x2 = GSL::Vector::linspace(0,2.4,20)
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#graph([x_vec,y_vec], [x2, coef.eval(x2)], "-C -g 3 -S 4")
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=end
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r = RSRuby.instance
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answ = r.smooth_spline(x,y, :df => 3)
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## to plot it!
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#r.plot(x,y, :ylab=>"instantaneous pi_zeros")
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#r.lines(answ['x'], answ['y'])
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#r.points(answ['x'], answ['y'])
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#sleep(8)
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answ['y'].last
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end
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def plateau_exponential(x,y)
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xvec = GSL::Vector.alloc(x)
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yvec = GSL::Vector.alloc(y)
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a2, b2, = GSL::Fit.linear(xvec, GSL::Sf::log(yvec))
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x2 = GSL::Vector.linspace(0, 1.2, 20)
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exp_a = GSL::Sf::exp(a2)
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out_y = exp_a*GSL::Sf::exp(b2*x2)
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raise NotImplementedError, "need to grab out the answer"
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#graph([xvec, yvec], [x2, exp_a*GSL::Sf::exp(b2*x2)], "-C -g 3 -S 4")
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end
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# returns a conservative (but close) estimate of pi_0 given sorted p-values
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# following Storey et al. 2003, PNAS.
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def pi_zero(sorted_pvals)
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plateau_height( *(pi_zero_hats(sorted_pvals)) )
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end
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# returns an array where the left values have been filled in using the
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# similar values on the right side of the distribution. These values are
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# pushed onto the end of the array in no guaranteed order.
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# extends a distribution on the left side where it is missing since
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# xcorr values <= 0.0 are not reported
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# **
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# * *
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# * *
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# *
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# *
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# *
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# Grabs the right tail from above and inverts it to the left side (less
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# than zero), creating a more full distribution. raises an ArgumentError
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# if values_chopped_at_zero.size == 0
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# this method would be more robust with some smoothing.
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# Method currently only meant for large amounts of data.
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# input data does not need to be sorted
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def extend_distribution_left_of_zero(values_chopped_at_zero)
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sz = values_chopped_at_zero.size
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raise ArgumentError, "array.size must be > 0" if sz == 0
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num_bins = (Math.log10(sz) * 100).round
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vec = VecD.new(values_chopped_at_zero)
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(bins, freqs) = vec.histogram(num_bins)
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start_i = 0
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freqs.each_with_index do |f,i|
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if f.is_a?(Numeric) && f > 0
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start_i = i
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break
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end
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end
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match_it = freqs[start_i]
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# get the index of the first frequency value less than the zero frequency
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index_to_chop_at = -1
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rev_freqs = freqs.reverse
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rev_freqs.each_with_index do |freq,rev_i|
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if match_it - rev_freqs[rev_i+1] <= 0
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index_to_chop_at = freqs.size - 1 - rev_i
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break
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end
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end
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cut_point = bins[index_to_chop_at]
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values_chopped_at_zero + values_chopped_at_zero.select {|v| v >= cut_point }.map {|v| cut_point - v }
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end
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# assumes the decoy_vals follows a normal distribution
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def p_values(target_vals, decoy_vals)
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(mean, stdev) = VecD.new(decoy_vals).sample_stats
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r = RSRuby.instance
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vec = VecD.new(target_vals)
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right_tailed = true
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vec.p_value_normal(mean, stdev, right_tailed)
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end
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def p_values_for_sequest(target_hits, decoy_hits)
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|
+
dh_vals = decoy_hits.map {|v| v.xcorr }
|
157
|
+
new_decoy_vals = PiZero.extend_distribution_left_of_zero(dh_vals)
|
158
|
+
#File.open("target.yml", 'w') {|out| out.puts new_decoy_vals.join(" ") }
|
159
|
+
#File.open("decoy.yml", 'w') {|out| out.puts target_hits.map {|v| v.xcorr }.join(" ") }
|
160
|
+
#abort 'checking'
|
161
|
+
p_values(target_hits.map {|v| v.xcorr}, new_decoy_vals )
|
162
|
+
end
|
163
|
+
|
164
|
+
# takes a list of booleans with true being a target hit and false being a
|
165
|
+
# decoy hit and returns the pi_zero using the smooth method
|
166
|
+
# Should be ordered from best to worst (i.e., one expects more true values
|
167
|
+
# at the beginning of the list)
|
168
|
+
def pi_zero_from_booleans(booleans)
|
169
|
+
targets = 0
|
170
|
+
decoys = 0
|
171
|
+
xs = []
|
172
|
+
ys = []
|
173
|
+
booleans.reverse.each_with_index do |v,index|
|
174
|
+
if v
|
175
|
+
targets += 1
|
176
|
+
else
|
177
|
+
decoys += 1
|
178
|
+
end
|
179
|
+
if decoys > 0
|
180
|
+
xs << index
|
181
|
+
ys << targets.to_f / decoys
|
182
|
+
end
|
183
|
+
end
|
184
|
+
ys.reverse!
|
185
|
+
plateau_height(xs, ys)
|
186
|
+
end
|
187
|
+
|
188
|
+
# Takes an array of doublets ([[int, int], [int, int]...]) where the first
|
189
|
+
# value is the number of target hits and the second is the number of decoy
|
190
|
+
# hits. Expects that best hits are at the beginning of the list. Assumes
|
191
|
+
# that each sum is a subset
|
192
|
+
# of the following group (shown as actual hits rather than number of hits):
|
193
|
+
#
|
194
|
+
# [[target, target, target, decoy], [target, target, target, decoy,
|
195
|
+
# target, decoy, target], [target, target, target, decoy, target,
|
196
|
+
# decoy, target, decoy, target, target]]
|
197
|
+
#
|
198
|
+
# This assumption may be relaxed somewhat and should still give good
|
199
|
+
# results.
|
200
|
+
def pi_zero_from_groups(array_of_doublets)
|
201
|
+
pi_zeros = []
|
202
|
+
array_of_doublets.reverse.each_cons(2) do |two_doublets|
|
203
|
+
bigger, smaller = two_doublets
|
204
|
+
bigger[0] = bigger[0] - smaller[0]
|
205
|
+
bigger[1] = bigger[1] - smaller[1]
|
206
|
+
bigger.map! {|v| v < 0 ? 0 : v }
|
207
|
+
if bigger[1] > 0
|
208
|
+
pi_zeros << (bigger[0].to_f / bigger[1])
|
209
|
+
end
|
210
|
+
end
|
211
|
+
pi_zeros.reverse!
|
212
|
+
xs = (0...(pi_zeros.size)).to_a
|
213
|
+
plateau_height(xs, pi_zeros)
|
214
|
+
end
|
215
|
+
|
216
|
+
end
|
217
|
+
|
218
|
+
|
219
|
+
end
|
220
|
+
|
221
|
+
if $0 == __FILE__
|
222
|
+
#xcorrs = IO.readlines("/home/jtprince/xcorr_hist/all_xcorrs.yada").first.chomp.split(/\s+/).map {|v| v.to_f }
|
223
|
+
#PiZero.p_values_for_sequest(
|
224
|
+
#File.open("newtail.yada", 'w') {|out| out.puts new_dist.join(" ") }
|
225
|
+
|
226
|
+
|
227
|
+
end
|
data/lib/qvalue.rb
ADDED
@@ -0,0 +1,152 @@
|
|
1
|
+
|
2
|
+
begin
|
3
|
+
require 'rsruby'
|
4
|
+
rescue LoadError
|
5
|
+
puts "You must have the rsruby gem installed to use the qvalue module"
|
6
|
+
puts $!
|
7
|
+
raise LoadError
|
8
|
+
end
|
9
|
+
require 'vec'
|
10
|
+
|
11
|
+
# Adapted from qvalue.R by Alan Dabney and John Storey which was LGPL licensed
|
12
|
+
|
13
|
+
class VecD
|
14
|
+
Default_lambdas = []
|
15
|
+
0.0.step(0.9,0.05) {|v| Default_lambdas << v }
|
16
|
+
|
17
|
+
Default_smooth_df = 3
|
18
|
+
|
19
|
+
# returns the pi_zero estimate by taking the fraction of all p-values above
|
20
|
+
# lambd and dividing by (1-lambd) and gauranteed to be <= 1
|
21
|
+
def pi_zero_at_lambda(lambd)
|
22
|
+
v = (self.select{|v| v >= lambd}.size.to_f/self.size) / (1 - lambd)
|
23
|
+
[v, 1].min
|
24
|
+
end
|
25
|
+
|
26
|
+
# returns a parallel array (VecI) of how many are <= in the array
|
27
|
+
# roughly: VecD[1,8,10,8,9,10].num_le => VecI[1, 3, 6, 3, 4, 6]
|
28
|
+
def num_le
|
29
|
+
hash = Hash.new {|h,k| h[k] = [] }
|
30
|
+
self.each_with_index do |v,i|
|
31
|
+
hash[v] << i
|
32
|
+
end
|
33
|
+
num_le_ar = []
|
34
|
+
sorted = self.sort
|
35
|
+
count = 0
|
36
|
+
sorted.each_with_index do |v,i|
|
37
|
+
back = 1
|
38
|
+
count += 1
|
39
|
+
if v == sorted[i-back]
|
40
|
+
while (sorted[i-back] == v)
|
41
|
+
num_le_ar[i-back] = count
|
42
|
+
back -= 1
|
43
|
+
end
|
44
|
+
else
|
45
|
+
num_le_ar[i] = count
|
46
|
+
end
|
47
|
+
end
|
48
|
+
ret = VecI.new(self.size)
|
49
|
+
num_le_ar.zip(sorted) do |n,v|
|
50
|
+
indices = hash[v]
|
51
|
+
indices.each do |i|
|
52
|
+
ret[i] = n
|
53
|
+
end
|
54
|
+
end
|
55
|
+
ret
|
56
|
+
end
|
57
|
+
|
58
|
+
Default_pi_zero_args = {:lambda_vals => Default_lambdas, :method => :smooth, :log_transform => false }
|
59
|
+
|
60
|
+
# returns the Pi_0 for given p-values (the values in self)
|
61
|
+
# lambda_vals = Float or Array of floats of size >= 4. value(s) within (0,1)
|
62
|
+
# A single value given then the pi_zero is calculated at that point,
|
63
|
+
# superceding the method or log_transform arguments
|
64
|
+
# method = :smooth or :bootstrap
|
65
|
+
# log_transform = true or false
|
66
|
+
def pi_zero(lambda_vals=Default_pi_zero_args[:lambda_vals], method=Default_pi_zero_args[:method], log_transform=Default_pi_zero_args[:log_transform])
|
67
|
+
if self.min < 0 || self.max > 1
|
68
|
+
raise ArgumentError, "p-values must be within [0,1)"
|
69
|
+
end
|
70
|
+
|
71
|
+
if lambda_vals.is_a? Numeric
|
72
|
+
lambda_vals = [lambda_vals]
|
73
|
+
end
|
74
|
+
if lambda_vals.size != 1 && lambda_vals.size < 4
|
75
|
+
raise ArgumentError, "#{tun_arg} must have 1 or 4 or more values"
|
76
|
+
end
|
77
|
+
if lambda_vals.any? {|v| v < 0 || v >= 1}
|
78
|
+
raise ArgumentError, "#{tun_arg} vals must be within [0,1)"
|
79
|
+
end
|
80
|
+
|
81
|
+
pi_zeros = lambda_vals.map {|val| self.pi_zero_at_lambda(val) }
|
82
|
+
if lambda_vals.size == 1
|
83
|
+
pi_zeros.first
|
84
|
+
else
|
85
|
+
case method
|
86
|
+
when :smooth
|
87
|
+
r = RSRuby.instance
|
88
|
+
calc_pi_zero = lambda do |_pi_zeros|
|
89
|
+
hash = r.smooth_spline(lambda_vals, _pi_zeros, :df => Default_smooth_df)
|
90
|
+
hash['y'][VecD.new(lambda_vals).max_indices.max]
|
91
|
+
end
|
92
|
+
if log_transform
|
93
|
+
pi_zeros.log_space {|log_vals| calc_pi_zero.call(log_vals) }
|
94
|
+
else
|
95
|
+
calc_pi_zero.call(pi_zeros)
|
96
|
+
end
|
97
|
+
when :bootstrap
|
98
|
+
min_pi0 = pi_zeros.min
|
99
|
+
lsz = lambda_vals.size
|
100
|
+
mse = VecD.new(lsz, 0)
|
101
|
+
pi0_boot = VecD.new(lsz, 0)
|
102
|
+
sz = self.size
|
103
|
+
100.times do # for(i in 1:100) {
|
104
|
+
p_boot = self.shuffle
|
105
|
+
(0...lsz).each do |i|
|
106
|
+
pi0_boot[i] = ( p_boot.select{|v| v > lambda_vals[i] }.size.to_f/p_boot.size ) / (1-lambda_vals[i])
|
107
|
+
end
|
108
|
+
mse = mse + ( (pi0_boot-min_pi0)**2 )
|
109
|
+
end
|
110
|
+
# pi0 <- min(pi0[mse==min(mse)])
|
111
|
+
pi_zero = pi_zeros.values_at(*(mse.min_indices)).min
|
112
|
+
[pi_zero,1].min
|
113
|
+
else
|
114
|
+
raise ArgumentError, ":pi_zero_method must be :smooth or :bootstrap!"
|
115
|
+
end
|
116
|
+
end
|
117
|
+
end
|
118
|
+
|
119
|
+
# Returns a VecD filled with parallel q-values
|
120
|
+
# assumes that vec is filled with p values
|
121
|
+
# see pi_zero method for arguments, these should be named as symbols in the
|
122
|
+
# pi_zero_args hash.
|
123
|
+
# robust = true or false an indicator of whether it is desired to make
|
124
|
+
# the estimate more robust for small p-values and
|
125
|
+
# a direct finite sample estimate of pFDR
|
126
|
+
# A q-value can be thought of as the global positive false discovery rate
|
127
|
+
# at a particular p-value
|
128
|
+
def qvalues(robust=false, pi_zero_args={})
|
129
|
+
sz = self.size
|
130
|
+
pi0_args = Default_pi_zero_args.merge(pi_zero_args)
|
131
|
+
self.pi_zero(*(pi0_args.values_at(:lambda_vals, :method, :log_transform)))
|
132
|
+
raise RuntimeError, "pi0 <= 0 ... check your p-values!!" if pi_zero <= 0
|
133
|
+
num_le_ar = self.num_le
|
134
|
+
qvalues =
|
135
|
+
if robust
|
136
|
+
den = self.map {|val| 1 - ((1 - val)**(sz)) }
|
137
|
+
self * (pi_zero * sz) / ( num_le_ar * den)
|
138
|
+
else
|
139
|
+
self * (pi_zero * sz) / num_le_ar
|
140
|
+
end
|
141
|
+
|
142
|
+
u_ar = self.order
|
143
|
+
|
144
|
+
qvalues[u_ar[sz-1]] = [qvalues[u_ar[sz-1]],1].min
|
145
|
+
(0...sz-1).each do |i|
|
146
|
+
qvalues[u_ar[i]] = [qvalues[u_ar[i]],qvalues[u_ar[i+1]],1].min
|
147
|
+
end
|
148
|
+
qvalues
|
149
|
+
end
|
150
|
+
end
|
151
|
+
|
152
|
+
|
data/lib/spec_id/mass.rb
CHANGED
@@ -310,6 +310,17 @@ class SpecID::Precision::Filter
|
|
310
310
|
[peps] # no decoy
|
311
311
|
end
|
312
312
|
|
313
|
+
if opts[:decoy_pi_zero]
|
314
|
+
if pep_sets.size < 2
|
315
|
+
raise ArgumentError, "must have a decoy validator for pi zero calculation!"
|
316
|
+
end
|
317
|
+
require 'pi_zero'
|
318
|
+
(_target, _decoy) = pep_sets
|
319
|
+
pvals = PiZero.p_values_for_sequest(*pep_sets).sort
|
320
|
+
pi_zero = PiZero.pi_zero(pvals)
|
321
|
+
opts[:decoy_pi_zero] = PiZero.pi_zero(pvals)
|
322
|
+
end
|
323
|
+
|
313
324
|
if opts[:proteins]
|
314
325
|
protein_validator = Validator::ProtFromPep.new
|
315
326
|
end
|
@@ -86,8 +86,6 @@ class SpecID::Precision::Prob
|
|
86
86
|
end
|
87
87
|
end
|
88
88
|
|
89
|
-
|
90
|
-
|
91
89
|
validators.delete(decoy_val)
|
92
90
|
other_validators = validators
|
93
91
|
|
@@ -101,13 +99,14 @@ class SpecID::Precision::Prob
|
|
101
99
|
n_count = 0
|
102
100
|
d_count = 0
|
103
101
|
|
102
|
+
|
104
103
|
# this is a peptide prophet
|
105
104
|
is_peptide_prophet =
|
106
105
|
if spec_id.peps.first.respond_to?(:fval) ; true
|
107
106
|
else ;false
|
108
107
|
end
|
109
108
|
|
110
|
-
use_q_value =
|
109
|
+
use_q_value = other_validators.any? {|v| v.class == Validator::QValue }
|
111
110
|
|
112
111
|
## ORDER THE PEPTIDE HITS:
|
113
112
|
ordered_peps =
|
@@ -12,7 +12,11 @@ module SpecID
|
|
12
12
|
|
13
13
|
COMMAND_LINE = {
|
14
14
|
:sort_by_init => ['--sort_by_init', "sort the proteins based on init probability"],
|
15
|
-
:
|
15
|
+
:perc_qval => ['--perc_qval', "use percolator q-values to calculate precision"],
|
16
|
+
:to_qvalues => ['--to_qvalues', "transform probabilities into q-values",
|
17
|
+
"(includes pi_0 correction)",
|
18
|
+
"uses PROB [TYPE] if given and supercedes",
|
19
|
+
"the prob validation type"],
|
16
20
|
:prob => ['--prob [TYPE]', "use prophet probabilites to calculate precision",
|
17
21
|
"TYPE = nsp [default] prophet nsp",
|
18
22
|
" (nsp also should be used for PeptideProphet results)",
|
@@ -95,7 +99,8 @@ module SpecID
|
|
95
99
|
op.separator ""
|
96
100
|
|
97
101
|
op.val_opt(:prob, opts)
|
98
|
-
op.val_opt(:
|
102
|
+
op.val_opt(:perc_qval, opts)
|
103
|
+
op.val_opt(:to_qvalues, opts)
|
99
104
|
op.val_opt(:decoy, opts)
|
100
105
|
op.val_opt(:pephits, opts) # sets opts[:ties] = false
|
101
106
|
op.val_opt(:digestion, opts)
|
@@ -129,6 +134,7 @@ module SpecID
|
|
129
134
|
#puts 'making background estimates with: top_per_aaseq_charge'
|
130
135
|
:top_per_aaseq_charge
|
131
136
|
end
|
137
|
+
|
132
138
|
opts[:validators] = Validator::Cmdline.prepare_validators(opts, !opts[:ties], opts[:interactive], postfilter, spec_id_obj)
|
133
139
|
|
134
140
|
if opts[:output].size == 0
|
@@ -63,7 +63,7 @@ module Proph
|
|
63
63
|
class PepSummary::Pep < Sequest::PepXML::SearchHit
|
64
64
|
# aaseq is defined in SearchHit
|
65
65
|
|
66
|
-
%w(probability fval ntt nmc massd prots).each do |guy|
|
66
|
+
%w(probability fval ntt nmc massd prots q_value).each do |guy|
|
67
67
|
self.add_member(guy)
|
68
68
|
end
|
69
69
|
|
@@ -122,7 +122,7 @@ end # Proph
|
|
122
122
|
|
123
123
|
|
124
124
|
|
125
|
-
Proph::Prot = Arrayclass.new(%w(protein_name probability n_indistinguishable_proteins percent_coverage unique_stripped_peptides group_sibling_id total_number_peptides pct_spectrum_ids description peps))
|
125
|
+
Proph::Prot = Arrayclass.new(%w(protein_name probability n_indistinguishable_proteins percent_coverage unique_stripped_peptides group_sibling_id total_number_peptides pct_spectrum_ids description peps q_value))
|
126
126
|
|
127
127
|
# note that 'description' is found in the element 'annotation', attribute 'protein_description'
|
128
128
|
# NOTE!: unique_stripped peptides is an array rather than + joined string
|
@@ -142,7 +142,7 @@ end
|
|
142
142
|
|
143
143
|
# this is a pep from a -prot.xml file
|
144
144
|
|
145
|
-
Proph::Prot::Pep = Arrayclass.new(%w(peptide_sequence charge initial_probability nsp_adjusted_probability weight is_nondegenerate_evidence n_enzymatic_termini n_sibling_peptides n_sibling_peptides_bin n_instances is_contributing_evidence calc_neutral_pep_mass modification_info prots))
|
145
|
+
Proph::Prot::Pep = Arrayclass.new(%w(peptide_sequence charge initial_probability nsp_adjusted_probability weight is_nondegenerate_evidence n_enzymatic_termini n_sibling_peptides n_sibling_peptides_bin n_instances is_contributing_evidence calc_neutral_pep_mass modification_info prots q_value))
|
146
146
|
|
147
147
|
class Proph::Prot::Pep
|
148
148
|
include SpecID::Pep
|
data/lib/spec_id/srf.rb
CHANGED
@@ -6,6 +6,8 @@ require 'fasta'
|
|
6
6
|
require 'mspire'
|
7
7
|
require 'set'
|
8
8
|
|
9
|
+
require 'core_extensions'
|
10
|
+
|
9
11
|
module BinaryReader
|
10
12
|
Null_char = "\0"[0] ## TODO: change for ruby 1.9 or 2.0
|
11
13
|
# extracts a string with all empty chars at the end stripped
|
@@ -178,6 +180,7 @@ class SRF
|
|
178
180
|
attr_accessor :base_name
|
179
181
|
# this is the global peptides array
|
180
182
|
attr_accessor :peps
|
183
|
+
MASCOT_HYDROGEN_MASS = 1.007276
|
181
184
|
|
182
185
|
attr_accessor :filtered_by_precursor_mass_tolerance
|
183
186
|
|
@@ -207,18 +210,92 @@ class SRF
|
|
207
210
|
sprintf("%.#{decimal_places}f", float)
|
208
211
|
end
|
209
212
|
|
213
|
+
# this mimicks the output of merge.pl from mascot
|
214
|
+
# The only difference is that this does not include the "\r\n"
|
215
|
+
# that is found after the peak lists, instead, it uses "\n" throughout the
|
216
|
+
# file (thinking that this is preferable to mixing newline styles!)
|
217
|
+
# note that Mass
|
218
|
+
# if no filename is given, will use base_name + '.mgf'
|
219
|
+
def to_mgf_file(filename=nil)
|
220
|
+
filename =
|
221
|
+
if filename ; filename
|
222
|
+
else
|
223
|
+
base_name + '.mgf'
|
224
|
+
end
|
225
|
+
h_plus = SpecID::MONO[:h_plus]
|
226
|
+
File.open(filename, 'wb') do |out|
|
227
|
+
dta_files.zip(index) do |dta, i_ar|
|
228
|
+
chrg = dta.charge
|
229
|
+
out.puts 'BEGIN IONS'
|
230
|
+
out.puts "TITLE=#{[base_name, *i_ar].push('dta').join('.')}"
|
231
|
+
out.puts "CHARGE=#{chrg}+"
|
232
|
+
out.puts "PEPMASS=#{(dta.mh+((chrg-1)*h_plus))/chrg}"
|
233
|
+
peak_ar = dta.peaks.unpack('e*')
|
234
|
+
(0...(peak_ar.size)).step(2) do |i|
|
235
|
+
out.puts( peak_ar[i,2].join(' ') )
|
236
|
+
end
|
237
|
+
out.puts ''
|
238
|
+
out.puts 'END IONS'
|
239
|
+
out.puts ''
|
240
|
+
end
|
241
|
+
end
|
242
|
+
end
|
243
|
+
|
210
244
|
# not given an out_folder, will make one with the basename
|
211
|
-
|
245
|
+
# compress may be: :zip, :tgz, or nil (no compression)
|
246
|
+
# :zip requires gem rubyzip to be installed and is *very* bloated
|
247
|
+
# as it writes out all the files first!
|
248
|
+
# :tgz requires gem archive-tar-minitar to be installed
|
249
|
+
def to_dta_files(out_folder=nil, compress=nil)
|
212
250
|
outdir =
|
213
251
|
if out_folder ; out_folder
|
214
252
|
else base_name
|
215
253
|
end
|
216
254
|
|
217
|
-
|
218
|
-
|
219
|
-
|
220
|
-
|
221
|
-
|
255
|
+
case compress
|
256
|
+
when :tgz
|
257
|
+
begin
|
258
|
+
require 'archive/tar/minitar'
|
259
|
+
rescue LoadError
|
260
|
+
abort "need gem 'archive-tar-minitar' installed' for tgz compression!\n#{$!}"
|
261
|
+
end
|
262
|
+
require 'archive/targz' # my own simplified interface!
|
263
|
+
require 'zlib'
|
264
|
+
names = index.map do |i_ar|
|
265
|
+
[outdir, '/', [base_name, *i_ar].join('.'), '.dta'].join('')
|
266
|
+
end
|
267
|
+
#Archive::Targz.archive_as_files(outdir + '.tgz', names, dta_file_data)
|
268
|
+
|
269
|
+
tgz = Zlib::GzipWriter.new(File.open(outdir + '.tgz', 'wb'))
|
270
|
+
|
271
|
+
Archive::Tar::Minitar::Output.open(tgz) do |outp|
|
272
|
+
dta_files.each_with_index do |dta_file, i|
|
273
|
+
Archive::Tar::Minitar.pack_as_file(names[i], dta_file.to_dta_file_data, outp)
|
274
|
+
end
|
275
|
+
end
|
276
|
+
when :zip
|
277
|
+
begin
|
278
|
+
require 'zip/zipfilesystem'
|
279
|
+
rescue LoadError
|
280
|
+
abort "need gem 'rubyzip' installed' for zip compression!\n#{$!}"
|
281
|
+
end
|
282
|
+
#begin ; require 'zip/zipfilesystem' ; rescue LoadError, "need gem 'rubyzip' installed' for zip compression!\n#{$!}" ; end
|
283
|
+
Zip::ZipFile.open(outdir + ".zip", Zip::ZipFile::CREATE) do |zfs|
|
284
|
+
dta_files.zip(index) do |dta,i_ar|
|
285
|
+
#zfs.mkdir(outdir)
|
286
|
+
zfs.get_output_stream(outdir + '/' + [base_name, *i_ar].join('.') + '.dta') do |out|
|
287
|
+
dta.write_dta_file(out)
|
288
|
+
#zfs.commit
|
289
|
+
end
|
290
|
+
end
|
291
|
+
end
|
292
|
+
else # no compression
|
293
|
+
FileUtils.mkpath(outdir)
|
294
|
+
Dir.chdir(outdir) do
|
295
|
+
dta_files.zip(index) do |dta,i_ar|
|
296
|
+
File.open([base_name, *i_ar].join('.') << '.dta', 'wb') do |out|
|
297
|
+
dta.write_dta_file(out)
|
298
|
+
end
|
222
299
|
end
|
223
300
|
end
|
224
301
|
end
|
@@ -626,13 +703,20 @@ class SRF::DTA
|
|
626
703
|
self
|
627
704
|
end
|
628
705
|
|
706
|
+
def to_dta_file_data
|
707
|
+
string = "#{mh.round_to(6)} #{charge}\r\n"
|
708
|
+
peak_ar = peaks.unpack('e*')
|
709
|
+
(0...(peak_ar.size)).step(2) do |i|
|
710
|
+
# %d is equivalent to floor, so we round by adding 0.5!
|
711
|
+
string << "#{peak_ar[i].round_to(4)} #{(peak_ar[i+1] + 0.5).floor}\r\n"
|
712
|
+
#string << peak_ar[i,2].join(' ') << "\r\n"
|
713
|
+
end
|
714
|
+
string
|
715
|
+
end
|
716
|
+
|
629
717
|
# write a class dta file to the io object
|
630
718
|
def write_dta_file(io)
|
631
|
-
io.print
|
632
|
-
peak_ar = peaks.unpack('e*')
|
633
|
-
(0...(peak_ar.size)).step(2) do |i|
|
634
|
-
io.print( peak_ar[i,2].join(' '), "\r\n" )
|
635
|
-
end
|
719
|
+
io.print to_dta_file_data
|
636
720
|
end
|
637
721
|
|
638
722
|
end
|
data/lib/validator/background.rb
CHANGED
@@ -29,6 +29,10 @@ class Validator::Background
|
|
29
29
|
min_in_window(data_vec, last_0_index, min_window_pre, min_window_post)
|
30
30
|
end
|
31
31
|
|
32
|
+
def plot(vec)
|
33
|
+
`graph #{vec.join(" ")} -a -T X`
|
34
|
+
end
|
35
|
+
|
32
36
|
# not really working right currently
|
33
37
|
def derivs(avg_points=15, min_window_pre=5, min_window_post=5)
|
34
38
|
data_vec = VecD[*@data]
|
data/lib/validator/cmdline.rb
CHANGED
@@ -74,6 +74,9 @@ class Validator::Cmdline
|
|
74
74
|
"then give the FILENAME (e.g., --decoy decoy.srg)",
|
75
75
|
"DTR = Decoy to Target Ratio (default: #{DEFAULTS[:decoy][:decoy_to_target_ratio]})",
|
76
76
|
"DOM = *true/false, decoy on match",],
|
77
|
+
:decoy_pi_zero => ["--decoy_pi_zero", "uses sequest Xcorrs to estimate the",
|
78
|
+
"percentage of incorrect target hits.",
|
79
|
+
"This over-rides any given DTR (above)"],
|
77
80
|
:tps => ["--tps <fasta>", "for a completely defined sample, this is the",
|
78
81
|
"fasta file containing the true protein hits"],
|
79
82
|
# may require digestion:
|
@@ -141,7 +144,8 @@ class Validator::Cmdline
|
|
141
144
|
end
|
142
145
|
opts[:validators].push([:prob, mthd])
|
143
146
|
},
|
144
|
-
:
|
147
|
+
:perc_qval => lambda {|ar, opts| opts[:validators].push([:perc_qval]) },
|
148
|
+
:to_qvalues => lambda {|ar, opts| opts[:validators].push([:to_qvalues]) },
|
145
149
|
:decoy => lambda {|ar, opts|
|
146
150
|
myargs = [:decoy]
|
147
151
|
first_arg = ar[0]
|
@@ -273,7 +277,43 @@ class Validator::Cmdline
|
|
273
277
|
# postfilter is one of :top_per_scan, :top_per_aaseq,
|
274
278
|
# :top_per_aaseq_charge (of which last two are subsets of scan)
|
275
279
|
def self.prepare_validators(opts, false_on_tie, interactive, postfilter, spec_id)
|
280
|
+
|
276
281
|
validator_args = opts[:validators]
|
282
|
+
if validator_args.any? {|v| v.first == :to_qvalues }
|
283
|
+
prob_val_args_ar = validator_args.select {|v| v.first == :prob }.first
|
284
|
+
prob_method =
|
285
|
+
if prob_val_args_ar && prob_val_args_ar[1]
|
286
|
+
prob_val_args_ar[1]
|
287
|
+
else
|
288
|
+
:probability
|
289
|
+
end
|
290
|
+
validator_args.reject! {|v| v.first == :prob }
|
291
|
+
|
292
|
+
require 'vec'
|
293
|
+
require 'qvalue'
|
294
|
+
|
295
|
+
# get a list of p-values
|
296
|
+
pvals = spec_id.peps.map do |pep|
|
297
|
+
val = 1.0 - pep.send(prob_method)
|
298
|
+
val = 1e-9 if val == 0
|
299
|
+
val
|
300
|
+
end
|
301
|
+
pvals = VecD.new(pvals)
|
302
|
+
#qvals = pvals.qvalues(false, :lambda_vals => 0.30 )
|
303
|
+
qvals = pvals.qvalues
|
304
|
+
qvals.zip(spec_id.peps) do |qval,pep|
|
305
|
+
pep.q_value = qval
|
306
|
+
end
|
307
|
+
end
|
308
|
+
|
309
|
+
validator_args.map! do |v|
|
310
|
+
if v.first == :to_qvalues || v.first == :perc_qval
|
311
|
+
[:qval]
|
312
|
+
else
|
313
|
+
v
|
314
|
+
end
|
315
|
+
end
|
316
|
+
|
277
317
|
correct_wins = !false_on_tie
|
278
318
|
need_false_to_total_ratio = []
|
279
319
|
need_frequency = []
|
@@ -37,8 +37,9 @@ describe 'filter_and_validate.rb on small bioworks file' do
|
|
37
37
|
end
|
38
38
|
end
|
39
39
|
|
40
|
+
############################ uncomment this::
|
40
41
|
# this ensures that the actual commandline version gives usage.
|
41
|
-
it_should_behave_like "a cmdline program"
|
42
|
+
# it_should_behave_like "a cmdline program"
|
42
43
|
|
43
44
|
it 'outputs to yaml' do
|
44
45
|
reply = @st_to_yaml.call( @args )
|
@@ -46,6 +47,7 @@ describe 'filter_and_validate.rb on small bioworks file' do
|
|
46
47
|
reply.keys.map {|v| v.to_s}.sort.should == keys
|
47
48
|
end
|
48
49
|
|
50
|
+
|
49
51
|
it 'responds to --prob init' do
|
50
52
|
normal = @st_to_yaml.call( @args + " --prob" )
|
51
53
|
|
@@ -69,6 +71,16 @@ describe 'filter_and_validate.rb on small bioworks file' do
|
|
69
71
|
end
|
70
72
|
end
|
71
73
|
|
74
|
+
it 'works with --to_qvalues flag' do
|
75
|
+
begin
|
76
|
+
normal = @st_to_yaml.call( @args + " --to_qvalues --prob" )
|
77
|
+
rescue RuntimeError
|
78
|
+
# right now the p values in this data set don't lend themselves to
|
79
|
+
# legitimate q-values, so we get a RuntimeError
|
80
|
+
# Need to work this one out
|
81
|
+
end
|
82
|
+
end
|
83
|
+
|
72
84
|
end
|
73
85
|
|
74
86
|
|
@@ -0,0 +1,104 @@
|
|
1
|
+
require File.expand_path( File.dirname(__FILE__) + '/spec_helper' )
|
2
|
+
require 'pi_zero'
|
3
|
+
|
4
|
+
describe PiZero do
|
5
|
+
before(:all) do
|
6
|
+
@bools = "11110010110101010101000001101010101001010010100001001010000010010000010010000010010101010101000001010000000010000000000100001000100000100000100000001000000000000100000000".split('').map do |v|
|
7
|
+
if v.to_i == 1
|
8
|
+
true
|
9
|
+
else
|
10
|
+
false
|
11
|
+
end
|
12
|
+
end
|
13
|
+
increment = 6.0 / @bools.size
|
14
|
+
@xcorrs = []
|
15
|
+
0.0.step(6.0, increment) {|v| @xcorrs << v }
|
16
|
+
@xcorrs.reverse!
|
17
|
+
|
18
|
+
@sorted_pvals = [0.0, 0.1, 0.223, 0.24, 0.55, 0.68, 0.68, 0.90, 0.98, 1.0]
|
19
|
+
end
|
20
|
+
|
21
|
+
it 'calculates instantaneous pi_0 hats' do
|
22
|
+
answ = PiZero.pi_zero_hats(@sorted_pvals, :step => 0.1)
|
23
|
+
exp_lambdas = [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9]
|
24
|
+
passing_threshold = [9, 8, 8, 6, 6, 6, 5, 3, 3, 2]
|
25
|
+
expected = passing_threshold.zip(exp_lambdas).map {|v,l| v.to_f / (10.0 * (1.0 - l)) }
|
26
|
+
(answ_lams, answ_pis) = answ
|
27
|
+
answ_lams.zip(exp_lambdas) {|a,e| a.should be_close(e, 0.0000000001) }
|
28
|
+
answ_pis.zip(expected) {|a,e| a.should be_close(e, 0.0000000001) }
|
29
|
+
end
|
30
|
+
|
31
|
+
xit 'can find a plateau height with exponential' do
|
32
|
+
x = [0.0, 0.01, 0.012, 0.13, 0.2, 0.3, 0.4, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2]
|
33
|
+
y = [1.0, 0.95, 0.92, 0.8, 0.7, 0.6, 0.55, 0.58, 0.62, 0.53, 0.54, 0.59, 0.4, 0.72]
|
34
|
+
|
35
|
+
z = PiZero.plateau_exponential(x,y)
|
36
|
+
# still working on this one
|
37
|
+
end
|
38
|
+
|
39
|
+
it 'can find a plateau height' do
|
40
|
+
x = [0.0, 0.01, 0.012, 0.13, 0.2, 0.3, 0.4, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2]
|
41
|
+
y = [1.0, 0.95, 0.92, 0.8, 0.7, 0.6, 0.55, 0.58, 0.62, 0.53, 0.54, 0.59, 0.4, 0.72]
|
42
|
+
z = PiZero.plateau_height(x,y)
|
43
|
+
z.should be_close(0.57, 0.05)
|
44
|
+
#require 'rsruby'
|
45
|
+
#r = RSRuby.instance
|
46
|
+
#r.plot(x,y)
|
47
|
+
#sleep(8)
|
48
|
+
end
|
49
|
+
|
50
|
+
it 'can calculate p values for SEQUEST hits' do
|
51
|
+
class FakeSequest ; attr_accessor :xcorr ; def initialize(xcorr) ; @xcorr = xcorr ; end ; end
|
52
|
+
|
53
|
+
target = []
|
54
|
+
decoy = []
|
55
|
+
cnt = 0
|
56
|
+
@xcorrs.zip(@bools) do |xcorr, bool|
|
57
|
+
if bool
|
58
|
+
target << FakeSequest.new(xcorr)
|
59
|
+
else
|
60
|
+
decoy << FakeSequest.new(xcorr)
|
61
|
+
end
|
62
|
+
end
|
63
|
+
pvalues = PiZero.p_values_for_sequest(target, decoy)
|
64
|
+
# frozen:
|
65
|
+
exp = [1.71344886775144e-07, 1.91226800512155e-07, 2.1332611415515e-07, 2.37879480495429e-07, 3.29004960353623e-07, 4.07557294032203e-07, 4.5332397295349e-07, 5.60147945165288e-07, 6.90985835582987e-07, 8.50958233458999e-07, 1.04621373866358e-06, 1.28412129273e-06, 2.35075612646546e-06, 2.59621031358335e-06, 3.16272156036349e-06, 3.84642913860656e-06, 4.67014790912829e-06, 5.66082984245324e-06, 7.53093419443452e-06, 9.09058296339405e-06, 1.20185706815653e-05, 1.44474800911154e-05, 2.27242185508328e-05, 2.967213280773e-05, 3.537451312629e-05, 5.93486219583748e-05, 7.64456599577934e-05, 0.000125433021038759, 0.000159783941297163, 0.000256431068540685, 0.000323066395099306, 0.00037608522266194, 0.000437091783629134, 0.000507167844234063, 0.000587522219112902, 0.000679502786805963, 0.00104103901250011, 0.00119624534498457, 0.00219153400681528, 0.00439503742960694, 0.00593498821589879, 0.00749365688957234, 0.0105069659581753, 0.0145259091109191, 0.0218905360424189, 0.0404530419122661]
|
66
|
+
pvalues.zip(exp) do |v,e|
|
67
|
+
v.should be_close(e, 0.000001)
|
68
|
+
end
|
69
|
+
end
|
70
|
+
|
71
|
+
it 'can calculate pi zero for target/decoy booleans' do
|
72
|
+
pi_zero = PiZero.pi_zero_from_booleans(@bools)
|
73
|
+
# frozen
|
74
|
+
pi_zero.should be_close(0.03522869, 0.0001)
|
75
|
+
end
|
76
|
+
|
77
|
+
it 'can calculate pi zero for groups of hits' do
|
78
|
+
# setup
|
79
|
+
targets = [4,3,8,3,5,3,4,5,4]
|
80
|
+
decoys = [0,2,2,3,5,7,8,8,8]
|
81
|
+
targets_summed = []
|
82
|
+
targets.each_with_index do |ar,i|
|
83
|
+
sum = 0
|
84
|
+
(0..i).each do |j|
|
85
|
+
sum += targets[j]
|
86
|
+
end
|
87
|
+
targets_summed << sum
|
88
|
+
end
|
89
|
+
decoys_summed = []
|
90
|
+
decoys.each_with_index do |ar,i|
|
91
|
+
sum = 0
|
92
|
+
(0..i).each do |j|
|
93
|
+
sum += decoys[j]
|
94
|
+
end
|
95
|
+
decoys_summed << sum
|
96
|
+
end
|
97
|
+
zipped = targets_summed.zip(decoys_summed)
|
98
|
+
pi_zero = PiZero.pi_zero_from_groups(zipped)
|
99
|
+
# frozen
|
100
|
+
pi_zero.should be_close(0.384064, 0.00001)
|
101
|
+
end
|
102
|
+
|
103
|
+
end
|
104
|
+
|
@@ -0,0 +1,39 @@
|
|
1
|
+
require File.expand_path( File.dirname(__FILE__) + '/spec_helper' )
|
2
|
+
|
3
|
+
require 'qvalue'
|
4
|
+
|
5
|
+
describe 'finding q-values' do
|
6
|
+
|
7
|
+
it 'can do num_le' do
|
8
|
+
x = VecD[1,8,10,8,9,10]
|
9
|
+
exp = VecD[1, 3, 6, 3, 4, 6]
|
10
|
+
x.num_le.should == exp
|
11
|
+
|
12
|
+
x = VecD[10,9,8,5,5,5,5,3,2]
|
13
|
+
exp = VecD[9, 8, 7, 6, 6, 6, 6, 2, 1]
|
14
|
+
x.num_le.should == exp
|
15
|
+
end
|
16
|
+
|
17
|
+
it 'can do qvalues with smooth pi0' do
|
18
|
+
pvals = VecD[0.00001, 0.0001, 0.001, 0.01, 0.03, 0.02, 0.01, 0.1, 0.2, 0.4, 0.5, 0.6, 0.77, 0.8, 0.99]
|
19
|
+
exp = [0.0000938637, 0.0004693185, 0.0031287899, 0.0187727394, 0.0402272988, 0.0312878991, 0.0187727394, 0.1173296215, 0.2085859937, 0.3754547887, 0.4266531690, 0.4693184859, 0.5363639839, 0.5363639839, 0.6195004014]
|
20
|
+
pvals.qvalues.zip(exp) do |a,b|
|
21
|
+
a.should be_close(b, 1.0e-9)
|
22
|
+
end
|
23
|
+
end
|
24
|
+
|
25
|
+
it 'can do qvalues with bootstrap pi0' do
|
26
|
+
puts "\nbootstrap pi0 needs further testing although answers seem to be close!"
|
27
|
+
pvals = VecD[0.00001, 0.0001, 0.001, 0.01, 0.03, 0.02, 0.01, 0.1, 0.2, 0.4, 0.5, 0.6, 0.77, 0.8, 0.99]
|
28
|
+
# this is what the Storey software gives for this:
|
29
|
+
# exp = [8.888889e-05, 4.444444e-04, 2.962963e-03, 1.777778e-02, 3.809524e-02, 2.962963e-02, 1.777778e-02, 1.111111e-01, 1.975309e-01, 3.555556e-01, 4.040404e-01, 4.444444e-01, 5.079365e-01, 5.079365e-01, 5.866667e-01]
|
30
|
+
exp = [9.38636971774565e-05, 0.000469318485887282, 0.00312878990591522, 0.0187727394354913, 0.0402272987903385, 0.0312878990591522, 0.0187727394354913, 0.117329621471821, 0.208585993727681, 0.375454788709826, 0.426653168988439, 0.469318485887282, 0.53636398387118, 0.53636398387118, 0.619500401371213]
|
31
|
+
robust = false
|
32
|
+
qvals = pvals.qvalues(robust, :method => :bootstrap)
|
33
|
+
qvals.zip(exp) do |a,b|
|
34
|
+
a.should be_close(b, 0.00001)
|
35
|
+
end
|
36
|
+
end
|
37
|
+
|
38
|
+
end
|
39
|
+
|
@@ -50,4 +50,18 @@ bias-prot: 37
|
|
50
50
|
# expecting were my best judgement (erring on the min side)
|
51
51
|
end
|
52
52
|
end
|
53
|
+
|
54
|
+
# This is where I'd like to go finding the plateau region!
|
55
|
+
#it 'finds the minimum of the plateu region of a stringency plot' do
|
56
|
+
# @data.each do |k,v|
|
57
|
+
# exp = @expected[k]
|
58
|
+
# bkg = Validator::Background.new(v)
|
59
|
+
# ans = bkg.quartile_deriv_finder
|
60
|
+
# ans.should be_close(v[exp], 0.01)
|
61
|
+
# # expecting were my best judgement (erring on the min side)
|
62
|
+
# end
|
63
|
+
#end
|
64
|
+
|
65
|
+
|
66
|
+
|
53
67
|
end
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: mspire
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.4.
|
4
|
+
version: 0.4.4
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- John Prince
|
@@ -9,7 +9,7 @@ autorequire:
|
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
11
|
|
12
|
-
date: 2008-
|
12
|
+
date: 2008-09-24 00:00:00 -06:00
|
13
13
|
default_executable:
|
14
14
|
dependencies:
|
15
15
|
- !ruby/object:Gem::Dependency
|
@@ -98,8 +98,10 @@ files:
|
|
98
98
|
- lib/ms/converter
|
99
99
|
- lib/ms/converter/mzxml.rb
|
100
100
|
- lib/ms/scan.rb
|
101
|
+
- lib/core_extensions.rb
|
101
102
|
- lib/scan_i.rb
|
102
103
|
- lib/fasta.rb
|
104
|
+
- lib/qvalue.rb
|
103
105
|
- lib/roc.rb
|
104
106
|
- lib/spec_id.rb
|
105
107
|
- lib/xml.rb
|
@@ -110,6 +112,7 @@ files:
|
|
110
112
|
- lib/transmem/phobius.rb
|
111
113
|
- lib/transmem/toppred.rb
|
112
114
|
- lib/ms.rb
|
115
|
+
- lib/pi_zero.rb
|
113
116
|
- lib/spec_id
|
114
117
|
- lib/spec_id/srf.rb
|
115
118
|
- lib/spec_id/sequest.rb
|
@@ -162,6 +165,8 @@ files:
|
|
162
165
|
- lib/validator/q_value.rb
|
163
166
|
- lib/xml_style_parser.rb
|
164
167
|
- lib/mspire.rb
|
168
|
+
- lib/archive
|
169
|
+
- lib/archive/targz.rb
|
165
170
|
- lib/spec_id_xml.rb
|
166
171
|
- lib/bsearch.rb
|
167
172
|
- bin/gi2annot.rb
|
@@ -204,12 +209,12 @@ files:
|
|
204
209
|
- script/simple_protein_digestion.rb
|
205
210
|
- script/peps_per_bin.rb
|
206
211
|
- specs/ms
|
207
|
-
- specs/ms/parser
|
208
212
|
- specs/ms/gradient_program_spec.rb
|
209
213
|
- specs/ms/parser_spec.rb
|
210
214
|
- specs/ms/spectrum_spec.rb
|
211
215
|
- specs/ms/msrun_spec.rb
|
212
216
|
- specs/merge_deep_spec.rb
|
217
|
+
- specs/qvalue_spec.rb
|
213
218
|
- specs/spec_helper.rb
|
214
219
|
- specs/fasta_spec.rb
|
215
220
|
- specs/transmem
|
@@ -241,6 +246,7 @@ files:
|
|
241
246
|
- specs/spec_id/digestor_spec.rb
|
242
247
|
- specs/spec_id/aa_freqs_spec.rb
|
243
248
|
- specs/rspec_autotest.rb
|
249
|
+
- specs/pi_zero_spec.rb
|
244
250
|
- specs/xml_spec.rb
|
245
251
|
- specs/sample_enzyme_spec.rb
|
246
252
|
- specs/transmem_spec_shared.rb
|
@@ -376,6 +382,7 @@ test_files:
|
|
376
382
|
- specs/ms/spectrum_spec.rb
|
377
383
|
- specs/ms/msrun_spec.rb
|
378
384
|
- specs/merge_deep_spec.rb
|
385
|
+
- specs/qvalue_spec.rb
|
379
386
|
- specs/fasta_spec.rb
|
380
387
|
- specs/transmem/phobius_spec.rb
|
381
388
|
- specs/transmem/toppred_spec.rb
|
@@ -396,6 +403,7 @@ test_files:
|
|
396
403
|
- specs/spec_id/sequest_spec.rb
|
397
404
|
- specs/spec_id/digestor_spec.rb
|
398
405
|
- specs/spec_id/aa_freqs_spec.rb
|
406
|
+
- specs/pi_zero_spec.rb
|
399
407
|
- specs/xml_spec.rb
|
400
408
|
- specs/sample_enzyme_spec.rb
|
401
409
|
- specs/gi_spec.rb
|