mspire 0.6.22 → 0.6.24

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data/Rakefile CHANGED
@@ -16,6 +16,8 @@ Jeweler::Tasks.new do |gem|
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16
  gem.add_dependency "bsearch", ">= 1.5.0"
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17
  gem.add_dependency "andand", ">= 1.3.1"
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18
  gem.add_dependency "obo", ">= 0.1.0"
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+ gem.add_dependency "builder", ">= 3.0.0"
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+ gem.add_dependency "trollop", ">= 1.16.2"
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21
  gem.add_development_dependency "rspec", "~> 2.6"
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22
  gem.add_development_dependency "jeweler", "~> 1.5.2"
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23
  gem.add_development_dependency "rcov", ">= 0"
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.6.22
1
+ 0.6.24
@@ -0,0 +1,93 @@
1
+ require 'yaml'
2
+
3
+ module MS
4
+ class Isotope
5
+ MEMBERS = [:atomic_number, :element, :mass_number, :atomic_mass, :relative_abundance, :average_mass, :mono]
6
+ MEMBERS.each {|key| attr_accessor key }
7
+
8
+ INFO_FILE = 'nist_isotope_info.yml'
9
+ INFO_FILE_FULL_PATH = File.expand_path(File.dirname(__FILE__) + "/isotope/#{INFO_FILE}")
10
+
11
+
12
+ def initialize(*args)
13
+ MEMBERS.zip(args) {|k,val| self.send("#{k}=", val) }
14
+ end
15
+
16
+ # Creates an isotope from a nist entry. Sets mono to false, which is not
17
+ # always correct (but needs to be corrected with additional info)
18
+ def self.from_nist_line(*args)
19
+ # atomic_number and mass_number are ints
20
+ [0,2].each {|i| args[i] = args[i].to_i }
21
+ # element is a downcase sym
22
+ args[1] = args[1].downcase.to_sym
23
+ # atomic_mass, relative_abundance, and average_mass as floats
24
+ [3, 4, 5].each {|i| args[i] = args[i][/([\w.]*)/].to_f }
25
+ # by default call every isotope the non-monoisotopic peak
26
+ # (will correct it as a group)
27
+ args << false
28
+ self.new(*args)
29
+ end
30
+
31
+ if File.exist?(INFO_FILE_FULL_PATH)
32
+
33
+ ISOTOPES = YAML.load_file(INFO_FILE_FULL_PATH).map {|ar| MS::Isotope.new *ar }
34
+ BY_ELEMENT = ISOTOPES.group_by(&:element)
35
+
36
+ else
37
+ unless __FILE__ == $0
38
+ warn "no file #{INFO_FILE_FULL_PATH} to read isotope information from"
39
+ warn "directly running the file: #{__FILE__}"
40
+ warn "will generate the file from NIST data"
41
+ end
42
+ end
43
+
44
+ class Updater
45
+ NIST_ISOTOPE_SITE = 'http://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=&all=all&ascii=ascii2&isotype=some'
46
+ class << self
47
+
48
+ def write_nist_info(filename)
49
+ isotopes = isotopes_from_nist_site
50
+ File.write(filename, isotopes.map {|isotope| MEMBERS.map {|key| isotope.send(key) }}.to_yaml)
51
+ end
52
+
53
+ def isotopes_from_nist_site(deuterium_is_kind_of_hydrogen=true)
54
+ require 'mechanize'
55
+ body = Mechanize.new.get(NIST_ISOTOPE_SITE).body.split("\n")
56
+ body.delete_if {|l| l[/^(<|\/)/]}
57
+ body.shift(22)
58
+ isotopes = body.each_slice(8).map do |lines|
59
+ arr = (1..4).to_a.map {|i| match lines[i] }
60
+ rel, avg = match(lines[5]), match(lines[6])
61
+ next if rel.nil?
62
+ rel.size > 0 ? Isotope.from_nist_line(*arr, rel, avg) : nil
63
+ end.compact!
64
+
65
+ # deuterium should be grouped with hydrogen, not as its own element!
66
+ isotopes.find {|iso| iso.element == :d }.element = :h if deuterium_is_kind_of_hydrogen
67
+
68
+ # update the mono boolean if this is the highest abundance peak
69
+ isotopes.group_by(&:element).values.each do |set|
70
+ set.max_by(&:relative_abundance).mono = true
71
+ end
72
+ isotopes
73
+ end
74
+
75
+ private
76
+
77
+ def match(string)
78
+ unless string.nil?
79
+ if string.empty?
80
+ nil
81
+ else
82
+ string[/= (.*)/,1]
83
+ end
84
+ end
85
+ end
86
+ end
87
+ end
88
+ end
89
+ end
90
+
91
+ if __FILE__ == $0
92
+ MS::Isotope::Updater.write_nist_info(MS::Isotope::INFO_FILE_FULL_PATH)
93
+ end
@@ -1,5 +1,6 @@
1
+
1
2
  module MS
2
- module Isotope
3
+ class Isotope
3
4
  module AA
4
5
  # These represent counts for the individual residues (i.e., no extra H
5
6
  # and OH on the ends)
@@ -0,0 +1,2017 @@
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+ ---
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