mspire-simulator 0.1.1 → 0.1.2
Sign up to get free protection for your applications and to get access to all the features.
- data/README.rdoc +1 -1
- data/Rakefile +1 -1
- data/VERSION +1 -1
- data/bin/mspire-simulator +2 -2
- data/bin/{sim_mail.rb → sim_mail} +0 -0
- data/lib/ms/rt/weka.rb +8 -2
- data/{bin → lib}/weka/M5P.model +0 -0
- data/{bin → lib}/weka/M5Rules.model +0 -0
- data/mspire-simulator.gemspec +5 -6
- metadata +5 -5
- data/bin/weka/weka.jar +0 -0
data/README.rdoc
CHANGED
@@ -7,7 +7,7 @@ Description:
|
|
7
7
|
gem install mspire-simulator
|
8
8
|
Dependencies:
|
9
9
|
ruby 1.9*
|
10
|
-
weka 3.6.0
|
10
|
+
weka 3.6.0 - May need to add to CLASSPATH see: http://weka.wikispaces.com/CLASSPATH+problems
|
11
11
|
fftw 3.2.2 - Tested in Linux Mint 12 and Ubuntu Oneiric Ocelot
|
12
12
|
== Examples
|
13
13
|
|
data/Rakefile
CHANGED
@@ -24,7 +24,7 @@ Jeweler::Tasks.new do |gem|
|
|
24
24
|
gem.add_dependency "obo", "= 0.1.0"
|
25
25
|
gem.add_dependency "trollop", "= 1.16.2"
|
26
26
|
|
27
|
-
gem.executables = ["mspire-simulator"]
|
27
|
+
gem.executables = ["mspire-simulator","sim_mail"]
|
28
28
|
gem.files.exclude "elution_curvefit.svg"
|
29
29
|
gem.files.exclude "intensity_var_curvefit.svg"
|
30
30
|
gem.files.exclude "lib/pool.rb"
|
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
|
-
0.1.
|
1
|
+
0.1.2
|
data/bin/mspire-simulator
CHANGED
@@ -120,8 +120,8 @@ module MspireSimulator
|
|
120
120
|
end
|
121
121
|
puts "Exception - Simulation Failed"
|
122
122
|
|
123
|
-
system "
|
123
|
+
system "sim_mail #{email} Exception - Simulation Failed" if email != "nil"
|
124
124
|
else
|
125
|
-
system "
|
125
|
+
system "sim_mail #{email} Success! - Simulation Complete" if email != "nil"
|
126
126
|
end
|
127
127
|
end
|
File without changes
|
data/lib/ms/rt/weka.rb
CHANGED
@@ -13,7 +13,10 @@ module MS
|
|
13
13
|
data<<pep.aa_counts
|
14
14
|
end
|
15
15
|
arff = make_rt_arff(Time.now.nsec.to_s,data)
|
16
|
-
|
16
|
+
|
17
|
+
path = Gem.bin_path('mspire-simulator', 'mspire-simulator').split(/\//)
|
18
|
+
dir = path[0..path.size-3].join("/")
|
19
|
+
system("java weka.classifiers.functions.MultilayerPerceptron -T #{arff} -l #{dir}/lib/weka/M5Rules.model -p 24 > #{arff}.out")
|
17
20
|
system("rm #{arff}")
|
18
21
|
|
19
22
|
#extract what was predicted by weka model
|
@@ -39,7 +42,10 @@ module MS
|
|
39
42
|
data << array.concat(pep.aa_counts)
|
40
43
|
end
|
41
44
|
arff = make_int_arff(Time.now.nsec.to_s,data)
|
42
|
-
|
45
|
+
|
46
|
+
path = Gem.bin_path('mspire-simulator', 'mspire-simulator').split(/\//)
|
47
|
+
dir = path[0..path.size-3].join("/")
|
48
|
+
system("java weka.classifiers.trees.M5P -T #{arff} -l #{dir}/lib/weka/M5P.model -p 27 > #{arff}.out")
|
43
49
|
system("rm #{arff}")
|
44
50
|
|
45
51
|
#extract what was predicted by weka model
|
data/{bin → lib}/weka/M5P.model
RENAMED
File without changes
|
File without changes
|
data/mspire-simulator.gemspec
CHANGED
@@ -5,14 +5,14 @@
|
|
5
5
|
|
6
6
|
Gem::Specification.new do |s|
|
7
7
|
s.name = "mspire-simulator"
|
8
|
-
s.version = "0.1.
|
8
|
+
s.version = "0.1.2"
|
9
9
|
|
10
10
|
s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
11
11
|
s.authors = ["anoyce"]
|
12
12
|
s.date = "2012-08-10"
|
13
13
|
s.description = "Simulates MS1 runs given amino acid FASTA files. Outputs an MZML file.\n\t\t\tCan simulate specific data if given an MZML file containing a single isolated peptide peak."
|
14
14
|
s.email = "andrewbnoyce@gmail.com"
|
15
|
-
s.executables = ["mspire-simulator"]
|
15
|
+
s.executables = ["mspire-simulator", "sim_mail"]
|
16
16
|
s.extra_rdoc_files = [
|
17
17
|
"LICENSE.txt",
|
18
18
|
"README.rdoc"
|
@@ -23,10 +23,7 @@ Gem::Specification.new do |s|
|
|
23
23
|
"Rakefile",
|
24
24
|
"VERSION",
|
25
25
|
"bin/mspire-simulator",
|
26
|
-
"bin/sim_mail
|
27
|
-
"bin/weka/M5P.model",
|
28
|
-
"bin/weka/M5Rules.model",
|
29
|
-
"bin/weka/weka.jar",
|
26
|
+
"bin/sim_mail",
|
30
27
|
"lib/ms/curvefit.rb",
|
31
28
|
"lib/ms/curvefit/curve_fit_helper.rb",
|
32
29
|
"lib/ms/curvefit/fit_graph.rb",
|
@@ -45,6 +42,8 @@ Gem::Specification.new do |s|
|
|
45
42
|
"lib/ms/sim_trollop.rb",
|
46
43
|
"lib/ms/tr_file_writer.rb",
|
47
44
|
"lib/progress.rb",
|
45
|
+
"lib/weka/M5P.model",
|
46
|
+
"lib/weka/M5Rules.model",
|
48
47
|
"mspire-simulator.gemspec",
|
49
48
|
"spec/file_writer_spec.rb",
|
50
49
|
"spec/merger_spec.rb",
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: mspire-simulator
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.1.
|
4
|
+
version: 0.1.2
|
5
5
|
prerelease:
|
6
6
|
platform: ruby
|
7
7
|
authors:
|
@@ -177,6 +177,7 @@ description: ! "Simulates MS1 runs given amino acid FASTA files. Outputs an MZML
|
|
177
177
|
email: andrewbnoyce@gmail.com
|
178
178
|
executables:
|
179
179
|
- mspire-simulator
|
180
|
+
- sim_mail
|
180
181
|
extensions: []
|
181
182
|
extra_rdoc_files:
|
182
183
|
- LICENSE.txt
|
@@ -187,10 +188,7 @@ files:
|
|
187
188
|
- Rakefile
|
188
189
|
- VERSION
|
189
190
|
- bin/mspire-simulator
|
190
|
-
- bin/sim_mail
|
191
|
-
- bin/weka/M5P.model
|
192
|
-
- bin/weka/M5Rules.model
|
193
|
-
- bin/weka/weka.jar
|
191
|
+
- bin/sim_mail
|
194
192
|
- lib/ms/curvefit.rb
|
195
193
|
- lib/ms/curvefit/curve_fit_helper.rb
|
196
194
|
- lib/ms/curvefit/fit_graph.rb
|
@@ -209,6 +207,8 @@ files:
|
|
209
207
|
- lib/ms/sim_trollop.rb
|
210
208
|
- lib/ms/tr_file_writer.rb
|
211
209
|
- lib/progress.rb
|
210
|
+
- lib/weka/M5P.model
|
211
|
+
- lib/weka/M5Rules.model
|
212
212
|
- mspire-simulator.gemspec
|
213
213
|
- spec/file_writer_spec.rb
|
214
214
|
- spec/merger_spec.rb
|
data/bin/weka/weka.jar
DELETED
Binary file
|