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 CHANGED
@@ -1,3 +1,7 @@
1
+ == 0.3.0 / 2009-05-25
2
+
3
+ * updates to use tap-0.17.0
4
+
1
5
  == 0.2.0 / 2009-03-31
2
6
 
3
7
  Updated release to use latest tap. Removed
@@ -1,10 +1,11 @@
1
+ require 'tap/tasks/file_task'
1
2
  require 'constants'
2
3
 
3
4
  module Ms
4
5
  module Xcalibur
5
6
  module Convert
6
7
 
7
- # :startdoc::manifest convert dta files to mgf format
8
+ # :startdoc::task convert dta files to mgf format
8
9
  #
9
10
  # Converts a set of dta files (Sequest format) into an mgf (Mascot format)
10
11
  # file. By default the mgf file is printed to $stdout, so redirection is
@@ -42,12 +43,12 @@ module Ms
42
43
  # calculated from the {constants}[bioactive.rubyforge.org/constants] gem to be
43
44
  # ~ 1.007276 Da
44
45
  #
45
- class DtaToMgf < Tap::FileTask
46
+ class DtaToMgf < Tap::Tasks::FileTask
46
47
  include Constants::Libraries
47
48
 
48
49
  # Returns the unrounded mass of a proton (H - e) as calculated
49
50
  # from the {constants}[bioactive.rubyforge.org/constants] gem.
50
- config :proton_mass, Element['H'].mass - Particle['Electron'].mass, &c.num_or_nil # Specify the proton mass
51
+ config :proton_mass, Element['H'].mass - Particle['Electron'].mass, &c.numeric_or_nil # Specify the proton mass
51
52
  config :output, $stdout, &c.io(:<<, :binmode) # The output file
52
53
 
53
54
  def process(*dta_files)
@@ -57,7 +58,7 @@ module Ms
57
58
 
58
59
  log :convert, "#{dta_files.length} dta files"
59
60
  dta_files.each do |file|
60
- check_terminate
61
+ app.check_terminate
61
62
  lines = File.read(file).split(/\r?\n/)
62
63
 
63
64
  # get the mh and z
@@ -79,6 +80,7 @@ END IONS
79
80
  }
80
81
  end
81
82
  end
83
+ output
82
84
  end
83
85
  end
84
86
  end
@@ -1,8 +1,10 @@
1
+ require 'tap/tasks/file_task'
2
+
1
3
  module Ms
2
4
  module Xcalibur
3
5
  module Convert
4
6
 
5
- # :startdoc::manifest convert RAW files to dta format
7
+ # :startdoc::task convert RAW files to dta format
6
8
  #
7
9
  # Converts a RAW file to dta files using extract_msn.exe. Returns an
8
10
  # array of the output dta files. By default extracted files are put
@@ -27,13 +29,13 @@ module Ms
27
29
  #
28
30
  # % tap run -- raw_to_dta --extract_msn_help
29
31
  #
30
- class RawToDta < Tap::FileTask
32
+ class RawToDta < Tap::Tasks::FileTask
31
33
  config :extract_msn, 'C:\Xcalibur\System\Programs\extract_msn.exe' # The full path to the extract_msn executable
32
34
  config :first_scan, nil, :short => :F, &c.integer_or_nil
33
35
  config :last_scan, nil, :short => :L, &c.integer_or_nil
34
- config :lower_MW, nil, :short => :B, &c.num_or_nil
35
- config :upper_MW, nil, :short => :T, &c.num_or_nil
36
- config :precursor_mass_tol, 1.4, :short => :M, &c.num
36
+ config :lower_MW, nil, :short => :B, &c.numeric_or_nil
37
+ config :upper_MW, nil, :short => :T, &c.numeric_or_nil
38
+ config :precursor_mass_tol, 1.4, :short => :M, &c.numeric
37
39
  config :num_allowed_intermediate_scans_for_grouping, 1, :short => :S, &c.integer
38
40
  config :charge_state, nil, :short => :C, &c.integer_or_nil
39
41
  config :num_required_group_scans, 1, :short => :G, &c.integer_or_nil
@@ -45,7 +47,7 @@ module Ms
45
47
  config :perform_charge_calculations, nil, :short => :K, &c.flag
46
48
  config :template_file, nil, :short => :O
47
49
  config :options_string, nil, :short => :A
48
- config :minimum_signal_to_noise, 3, :short => :R, &c.num
50
+ config :minimum_signal_to_noise, 3, :short => :R, &c.numeric
49
51
  config :minimum_number_of_peaks, 5, :short => :r, &c.integer
50
52
 
51
53
  config :output_dir, nil, &c.string_or_nil # The output directory
@@ -1,8 +1,9 @@
1
+ require 'tap/tasks/file_task'
1
2
  require 'ms/xcalibur/peak_file'
2
3
 
3
4
  module Ms
4
5
  module Xcalibur
5
- # :startdoc::manifest adds graph data to an exported peak file
6
+ # :startdoc::task adds graph data to an exported peak file
6
7
  #
7
8
  # Peakify adds points to signify the relative intensity (ie the rounded
8
9
  # intensity/max_intensity) of peaks to a peak list extracted from Xcalibur
@@ -24,18 +25,18 @@ module Ms
24
25
  # Options can be specified to filter out points within a range of relative
25
26
  # intensities.
26
27
  #
27
- class Peakify < Tap::FileTask
28
+ class Peakify < Tap::Tasks::FileTask
28
29
 
29
30
  config :point_char, '.' # A character used for each intensity point
30
- config :min, 0, &c.num # Min relative intenisty
31
- config :max, 100, &c.num # Max relative intenisty
31
+ config :min, 0, &c.numeric # Min relative intenisty
32
+ config :max, 100, &c.numeric # Max relative intenisty
32
33
  config :sort, false, &c.flag # Sort by intensity
33
34
  config :output, $stdout, &c.io(:<<, :binmode) # The output file
34
35
 
35
36
  def process(source)
36
37
  prepare(output) if output.kind_of?(String)
37
- open_io(output, 'w') do |target|
38
- target.binmode
38
+ open_io(output, 'w') do |target|
39
+ target.binmode
39
40
 
40
41
  # now perform the task...
41
42
  peak_file = PeakFile.parse File.read(source)
@@ -59,6 +60,7 @@ module Ms
59
60
 
60
61
  target << peak_file.to_s
61
62
  end
63
+ output
62
64
  end
63
65
  end
64
66
  end
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: ms-xcalibur
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.2.0
4
+ version: 0.3.0
5
5
  platform: ruby
6
6
  authors:
7
7
  - Simon Chiang
@@ -9,28 +9,28 @@ autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
11
 
12
- date: 2009-03-31 00:00:00 -06:00
12
+ date: 2009-05-25 00:00:00 -06:00
13
13
  default_executable:
14
14
  dependencies:
15
15
  - !ruby/object:Gem::Dependency
16
- name: configurable
16
+ name: tap
17
17
  type: :runtime
18
18
  version_requirement:
19
19
  version_requirements: !ruby/object:Gem::Requirement
20
20
  requirements:
21
21
  - - ">="
22
22
  - !ruby/object:Gem::Version
23
- version: 0.4.2
23
+ version: 0.17.0
24
24
  version:
25
25
  - !ruby/object:Gem::Dependency
26
- name: tap
26
+ name: tap-tasks
27
27
  type: :runtime
28
28
  version_requirement:
29
29
  version_requirements: !ruby/object:Gem::Requirement
30
30
  requirements:
31
31
  - - ">="
32
32
  - !ruby/object:Gem::Version
33
- version: 0.12.4
33
+ version: 0.2.0
34
34
  version:
35
35
  - !ruby/object:Gem::Dependency
36
36
  name: constants
@@ -42,6 +42,16 @@ dependencies:
42
42
  - !ruby/object:Gem::Version
43
43
  version: "0.1"
44
44
  version:
45
+ - !ruby/object:Gem::Dependency
46
+ name: tap-test
47
+ type: :development
48
+ version_requirement:
49
+ version_requirements: !ruby/object:Gem::Requirement
50
+ requirements:
51
+ - - ">="
52
+ - !ruby/object:Gem::Version
53
+ version: 0.1.0
54
+ version:
45
55
  description:
46
56
  email: simon.a.chiang@gmail.com
47
57
  executables: []