ms-xcalibur 0.2.0 → 0.3.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/History +4 -0
- data/lib/ms/xcalibur/convert/dta_to_mgf.rb +6 -4
- data/lib/ms/xcalibur/convert/raw_to_dta.rb +8 -6
- data/lib/ms/xcalibur/peakify.rb +8 -6
- metadata +16 -6
data/History
CHANGED
@@ -1,10 +1,11 @@
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require 'tap/tasks/file_task'
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require 'constants'
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module Ms
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module Xcalibur
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module Convert
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-
# :startdoc::
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# :startdoc::task convert dta files to mgf format
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#
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# Converts a set of dta files (Sequest format) into an mgf (Mascot format)
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# file. By default the mgf file is printed to $stdout, so redirection is
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@@ -42,12 +43,12 @@ module Ms
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# calculated from the {constants}[bioactive.rubyforge.org/constants] gem to be
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# ~ 1.007276 Da
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#
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class DtaToMgf < Tap::FileTask
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class DtaToMgf < Tap::Tasks::FileTask
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include Constants::Libraries
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# Returns the unrounded mass of a proton (H - e) as calculated
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# from the {constants}[bioactive.rubyforge.org/constants] gem.
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config :proton_mass, Element['H'].mass - Particle['Electron'].mass, &c.
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config :proton_mass, Element['H'].mass - Particle['Electron'].mass, &c.numeric_or_nil # Specify the proton mass
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config :output, $stdout, &c.io(:<<, :binmode) # The output file
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def process(*dta_files)
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@@ -57,7 +58,7 @@ module Ms
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log :convert, "#{dta_files.length} dta files"
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dta_files.each do |file|
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check_terminate
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app.check_terminate
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lines = File.read(file).split(/\r?\n/)
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# get the mh and z
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@@ -79,6 +80,7 @@ END IONS
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}
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end
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end
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output
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end
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end
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end
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@@ -1,8 +1,10 @@
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require 'tap/tasks/file_task'
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module Ms
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module Xcalibur
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module Convert
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-
# :startdoc::
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# :startdoc::task convert RAW files to dta format
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#
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# Converts a RAW file to dta files using extract_msn.exe. Returns an
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# array of the output dta files. By default extracted files are put
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@@ -27,13 +29,13 @@ module Ms
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#
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# % tap run -- raw_to_dta --extract_msn_help
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#
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class RawToDta < Tap::FileTask
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class RawToDta < Tap::Tasks::FileTask
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config :extract_msn, 'C:\Xcalibur\System\Programs\extract_msn.exe' # The full path to the extract_msn executable
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config :first_scan, nil, :short => :F, &c.integer_or_nil
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config :last_scan, nil, :short => :L, &c.integer_or_nil
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config :lower_MW, nil, :short => :B, &c.
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config :upper_MW, nil, :short => :T, &c.
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config :precursor_mass_tol, 1.4, :short => :M, &c.
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config :lower_MW, nil, :short => :B, &c.numeric_or_nil
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config :upper_MW, nil, :short => :T, &c.numeric_or_nil
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config :precursor_mass_tol, 1.4, :short => :M, &c.numeric
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config :num_allowed_intermediate_scans_for_grouping, 1, :short => :S, &c.integer
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config :charge_state, nil, :short => :C, &c.integer_or_nil
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config :num_required_group_scans, 1, :short => :G, &c.integer_or_nil
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@@ -45,7 +47,7 @@ module Ms
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config :perform_charge_calculations, nil, :short => :K, &c.flag
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config :template_file, nil, :short => :O
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config :options_string, nil, :short => :A
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config :minimum_signal_to_noise, 3, :short => :R, &c.
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config :minimum_signal_to_noise, 3, :short => :R, &c.numeric
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config :minimum_number_of_peaks, 5, :short => :r, &c.integer
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config :output_dir, nil, &c.string_or_nil # The output directory
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data/lib/ms/xcalibur/peakify.rb
CHANGED
@@ -1,8 +1,9 @@
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require 'tap/tasks/file_task'
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require 'ms/xcalibur/peak_file'
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module Ms
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module Xcalibur
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# :startdoc::
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# :startdoc::task adds graph data to an exported peak file
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#
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# Peakify adds points to signify the relative intensity (ie the rounded
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# intensity/max_intensity) of peaks to a peak list extracted from Xcalibur
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@@ -24,18 +25,18 @@ module Ms
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# Options can be specified to filter out points within a range of relative
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# intensities.
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#
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class Peakify < Tap::FileTask
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class Peakify < Tap::Tasks::FileTask
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config :point_char, '.' # A character used for each intensity point
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config :min, 0, &c.
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config :max, 100, &c.
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config :min, 0, &c.numeric # Min relative intenisty
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config :max, 100, &c.numeric # Max relative intenisty
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config :sort, false, &c.flag # Sort by intensity
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config :output, $stdout, &c.io(:<<, :binmode) # The output file
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def process(source)
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prepare(output) if output.kind_of?(String)
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open_io(output, 'w') do |target|
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target.binmode
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open_io(output, 'w') do |target|
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target.binmode
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# now perform the task...
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peak_file = PeakFile.parse File.read(source)
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@@ -59,6 +60,7 @@ module Ms
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target << peak_file.to_s
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end
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output
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end
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end
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end
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metadata
CHANGED
@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: ms-xcalibur
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version: !ruby/object:Gem::Version
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version: 0.
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version: 0.3.0
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platform: ruby
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authors:
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- Simon Chiang
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bindir: bin
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cert_chain: []
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date: 2009-
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date: 2009-05-25 00:00:00 -06:00
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default_executable:
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dependencies:
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- !ruby/object:Gem::Dependency
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name:
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name: tap
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type: :runtime
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version_requirement:
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: 0.
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version: 0.17.0
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version:
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- !ruby/object:Gem::Dependency
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name: tap
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name: tap-tasks
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type: :runtime
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version_requirement:
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: 0.
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version: 0.2.0
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version:
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- !ruby/object:Gem::Dependency
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name: constants
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- !ruby/object:Gem::Version
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version: "0.1"
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version:
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- !ruby/object:Gem::Dependency
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name: tap-test
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type: :development
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version_requirement:
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: 0.1.0
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version:
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description:
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email: simon.a.chiang@gmail.com
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executables: []
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