mspire-sequest 0.2.6 → 0.2.7

Sign up to get free protection for your applications and to get access to all the features.
Files changed (6) hide show
  1. data/History +4 -0
  2. data/README.rdoc +31 -23
  3. data/Rakefile +5 -5
  4. data/VERSION +1 -1
  5. data/spec/mspire/sequest/srf/pepxml_spec.rb +2 -1
  6. metadata +13 -13
data/History CHANGED
@@ -1,3 +1,7 @@
1
+ == 0.2.7 / 2011-09-13
2
+
3
+ Works with mspire libraries. Updated dependencies.
4
+
1
5
  == 0.2.0 / 2011-09-13
2
6
 
3
7
  Breaking backwards compatbility. Based on new msplat gem instead of ms-core, ms-ident, etc. MS module instead of Ms module.
data/README.rdoc CHANGED
@@ -1,8 +1,12 @@
1
- = ms-sequest
1
+ = mspire-sequest
2
2
 
3
3
  An {mspire}[http://mspire.rubyforge.org] library supporting SEQUEST, Bioworks, SQT and associated formats.
4
4
 
5
- == {Current API}[http://rubydoc.info/gems/ms-sequest]
5
+ == {Current API}[http://rubydoc.info/gems/mspire-sequest]
6
+
7
+ == Cite
8
+
9
+ Prince JT, Marcotte EM. <b>mspire: mass spectrometry proteomics in Ruby.</b> *Bioinformatics.* 2008 Dec 1;24(23):2796-7. ({pubmed}[http://www.ncbi.nlm.nih.gov/pubmed/18930952])
6
10
 
7
11
  == Examples
8
12
 
@@ -10,38 +14,42 @@ Provides two executables for extracting information from an Srf file (run withou
10
14
 
11
15
  srf_to_sqt.rb file.srf # => file.sqt
12
16
  srf_to_search.rb file.srf # => file.mgf (also can make .dta files)
17
+ srf_to_pepxml.rb file.srf # => file.xml (pepxml file)
13
18
 
14
- === MS::Sequest::Srf
19
+ === Mspire::Sequest::Srf
15
20
 
16
21
  Can read and convert Bioworks Sequest Results Files (SRF).
17
22
 
18
- require 'ms/sequest/srf'
19
- srf = MS::Sequest::Srf.new("file.srf")
23
+ require 'mspire/sequest/srf'
24
+ srf = Mspire::Sequest::Srf.new("file.srf")
20
25
 
21
26
  Conversions (see api for options):
22
27
 
23
- require 'ms/sequest/srf/sqt' # require this in addition to 'ms/sequest/srf'
28
+ require 'mspire/sequest/srf/sqt' # require this in addition to 'mspire/sequest/srf'
24
29
  srf.to_sqt # (outputs a file) -> file.sqt
25
30
 
26
- require 'ms/sequest/srf/search' # require this in addition to 'ms/sequest/srf'
31
+ require 'mspire/sequest/srf/search' # require this in addition to 'mspire/sequest/srf'
27
32
  srf.to_mgf # (outputs a file) -> file.mgf
28
33
  srf.to_dta # (outputs a dir) -> file
29
34
  srf.to_dta("file.tgz", :tgz) # on the fly tgz (requires archive-tar-minitar)
30
35
 
31
- Object access (see MS::Sequest::Srf for much more):
36
+ require 'mspire/sequest/srf/pepxml' # require this in addition to 'mspire/sequest/srf'
37
+ srf.to_pepxml # (outputs a file) -> file.xml
38
+
39
+ Object access (see Mspire::Sequest::Srf for much more):
32
40
 
33
- srf.header # MS::Sequest::Srf::Header object
34
- srf.params # MS::Sequest::Params object
35
- srf.dta_files # MS::Sequest::Srf::Dta objects
36
- srf.out_files # MS::Sequest::Srf::Out objects
37
- srf.peptide_hits # MS::Sequest::Srf::Out::Peptide objects
41
+ srf.header # Mspire::Sequest::Srf::Header object
42
+ srf.params # Mspire::Sequest::Params object
43
+ srf.dta_files # Mspire::Sequest::Srf::Dta objects
44
+ srf.out_files # Mspire::Sequest::Srf::Out objects
45
+ srf.peptide_hits # Mspire::Sequest::Srf::Out::Peptide objects
38
46
 
39
- === MS::Sequest::Params
47
+ === Mspire::Sequest::Params
40
48
 
41
49
  Object or hash access to any parameter in the file. Also provides a unified interface across several versions (3.1 - 3.3)
42
50
 
43
- require 'ms/sequest/params'
44
- params = MS::Sequest::Params.new("sequest.params")
51
+ require 'mspire/sequest/params'
52
+ params = Mspire::Sequest::Params.new("sequest.params")
45
53
  params.any_existing_param # -> some value or empty string if no value
46
54
  params['any_existing_param'] # -> some value or empty string if no value
47
55
  params.non_existent_param # -> nil
@@ -53,13 +61,13 @@ Object or hash access to any parameter in the file. Also provides a unified int
53
61
  params.precursor_mass_type # => "average" | "monoisotopic"
54
62
  params.fragment_mass_type # => "average" | "monoisotopic"
55
63
 
56
- === MS::Sequest::Sqt
64
+ === Mspire::Sequest::Sqt
57
65
 
58
- sqt = MS::Sequest::Sqt.new("file.sqt")
66
+ sqt = Mspire::Sequest::Sqt.new("file.sqt")
59
67
  sqt.header
60
- sqt.spectra.each do |spectrum| # an MS::Sequest::Sqt::Spectrum object
61
- spectrum.matches.each do |match| # an MS::Sequest::Sqt::Match object
62
- match.loci.each do |locus| # an MS::Sequest::Sqt::Locus object
68
+ sqt.spectra.each do |spectrum| # an Mspire::Sequest::Sqt::Spectrum object
69
+ spectrum.matches.each do |match| # an Mspire::Sequest::Sqt::Match object
70
+ match.loci.each do |locus| # an Mspire::Sequest::Sqt::Locus object
63
71
  end
64
72
  end
65
73
  end
@@ -69,7 +77,7 @@ Object or hash access to any parameter in the file. Also provides a unified int
69
77
 
70
78
  Also reads Percolator SQT output files intelligently:
71
79
 
72
- psqt = MS::Sequest::Sqt.new("percolator_output.sqt")
80
+ psqt = Mspire::Sequest::Sqt.new("percolator_output.sqt")
73
81
  psqt.peptide_hits.each do |pmatch|
74
82
  pmatch.percolator_score == pmatch.xcorr
75
83
  pmatch.negative_q_value == pmatch.sp
@@ -78,7 +86,7 @@ Also reads Percolator SQT output files intelligently:
78
86
 
79
87
  == Installation
80
88
 
81
- gem install ms-sequest
89
+ gem install mspire-sequest
82
90
 
83
91
  == Copyright
84
92
 
data/Rakefile CHANGED
@@ -11,12 +11,12 @@ Jeweler::Tasks.new do |gem|
11
11
  gem.email = "jtprince@gmail.com"
12
12
  gem.authors = ["John T. Prince"]
13
13
  gem.rubyforge_project = 'mspire'
14
- gem.add_runtime_dependency "mspire", "= 0.8.1"
15
- gem.add_runtime_dependency "trollop", "~> 1.16"
16
- gem.add_development_dependency "jeweler", "~> 1.5.2"
17
- gem.add_development_dependency "bio", "~> 1.4.2"
14
+ gem.add_runtime_dependency "mspire", "= 0.8.5"
15
+ gem.add_runtime_dependency "trollop", "~> 2.0.0"
16
+ gem.add_development_dependency "jeweler", "~> 1.8.4"
17
+ gem.add_development_dependency "bio", "~> 1.4.3"
18
18
  gem.add_development_dependency "ms-testdata", "= 0.2.1"
19
- gem.add_development_dependency "rspec", "~> 2.8.0"
19
+ gem.add_development_dependency "rspec", "~> 2.12.0"
20
20
  end
21
21
  Jeweler::RubygemsDotOrgTasks.new
22
22
 
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.2.6
1
+ 0.2.7
data/spec/mspire/sequest/srf/pepxml_spec.rb CHANGED
@@ -57,12 +57,13 @@ describe 'an Mspire::Ident::Pepxml object from an srf file with modifications' d
57
57
 
58
58
  it 'gets everything right' do
59
59
  xml_string = @srf.to_pepxml(:verbose => false).to_xml
60
+
60
61
  doc = Nokogiri::XML.parse(xml_string, nil, nil, Nokogiri::XML::ParseOptions::DEFAULT_XML | Nokogiri::XML::ParseOptions::NOBLANKS)
61
62
 
62
63
  root = doc.root
63
64
 
64
65
  root.name.should == "msms_pipeline_analysis"
65
- has_attributes( root, 'schemaLocation="http://regis-web.systemsbiology.net/pepXML /tools/bin/TPP/tpp/schema/pepXML_v115.xsd"' )
66
+ has_attributes( root, 'xsi:schemaLocation="http://regis-web.systemsbiology.net/pepXML /tools/bin/TPP/tpp/schema/pepXML_v115.xsd"' )
66
67
  root['date'].should_not be_nil
67
68
  root['summary_xml'].should match( "020.xml" )
68
69
  root.namespaces.should == ( {"xmlns" => "http://regis-web.systemsbiology.net/pepXML" } )
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: mspire-sequest
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.2.6
4
+ version: 0.2.7
5
5
  prerelease:
6
6
  platform: ruby
7
7
  authors:
@@ -9,7 +9,7 @@ authors:
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2012-07-25 00:00:00.000000000 Z
12
+ date: 2012-12-18 00:00:00.000000000 Z
13
13
  dependencies:
14
14
  - !ruby/object:Gem::Dependency
15
15
  name: mspire
@@ -18,7 +18,7 @@ dependencies:
18
18
  requirements:
19
19
  - - '='
20
20
  - !ruby/object:Gem::Version
21
- version: 0.8.1
21
+ version: 0.8.5
22
22
  type: :runtime
23
23
  prerelease: false
24
24
  version_requirements: !ruby/object:Gem::Requirement
@@ -26,7 +26,7 @@ dependencies:
26
26
  requirements:
27
27
  - - '='
28
28
  - !ruby/object:Gem::Version
29
- version: 0.8.1
29
+ version: 0.8.5
30
30
  - !ruby/object:Gem::Dependency
31
31
  name: trollop
32
32
  requirement: !ruby/object:Gem::Requirement
@@ -34,7 +34,7 @@ dependencies:
34
34
  requirements:
35
35
  - - ~>
36
36
  - !ruby/object:Gem::Version
37
- version: '1.16'
37
+ version: 2.0.0
38
38
  type: :runtime
39
39
  prerelease: false
40
40
  version_requirements: !ruby/object:Gem::Requirement
@@ -42,7 +42,7 @@ dependencies:
42
42
  requirements:
43
43
  - - ~>
44
44
  - !ruby/object:Gem::Version
45
- version: '1.16'
45
+ version: 2.0.0
46
46
  - !ruby/object:Gem::Dependency
47
47
  name: jeweler
48
48
  requirement: !ruby/object:Gem::Requirement
@@ -50,7 +50,7 @@ dependencies:
50
50
  requirements:
51
51
  - - ~>
52
52
  - !ruby/object:Gem::Version
53
- version: 1.5.2
53
+ version: 1.8.4
54
54
  type: :development
55
55
  prerelease: false
56
56
  version_requirements: !ruby/object:Gem::Requirement
@@ -58,7 +58,7 @@ dependencies:
58
58
  requirements:
59
59
  - - ~>
60
60
  - !ruby/object:Gem::Version
61
- version: 1.5.2
61
+ version: 1.8.4
62
62
  - !ruby/object:Gem::Dependency
63
63
  name: bio
64
64
  requirement: !ruby/object:Gem::Requirement
@@ -66,7 +66,7 @@ dependencies:
66
66
  requirements:
67
67
  - - ~>
68
68
  - !ruby/object:Gem::Version
69
- version: 1.4.2
69
+ version: 1.4.3
70
70
  type: :development
71
71
  prerelease: false
72
72
  version_requirements: !ruby/object:Gem::Requirement
@@ -74,7 +74,7 @@ dependencies:
74
74
  requirements:
75
75
  - - ~>
76
76
  - !ruby/object:Gem::Version
77
- version: 1.4.2
77
+ version: 1.4.3
78
78
  - !ruby/object:Gem::Dependency
79
79
  name: ms-testdata
80
80
  requirement: !ruby/object:Gem::Requirement
@@ -98,7 +98,7 @@ dependencies:
98
98
  requirements:
99
99
  - - ~>
100
100
  - !ruby/object:Gem::Version
101
- version: 2.8.0
101
+ version: 2.12.0
102
102
  type: :development
103
103
  prerelease: false
104
104
  version_requirements: !ruby/object:Gem::Requirement
@@ -106,7 +106,7 @@ dependencies:
106
106
  requirements:
107
107
  - - ~>
108
108
  - !ruby/object:Gem::Version
109
- version: 2.8.0
109
+ version: 2.12.0
110
110
  description: reads .SRF, .SQT and supports conversions
111
111
  email: jtprince@gmail.com
112
112
  executables:
@@ -178,7 +178,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
178
178
  version: '0'
179
179
  requirements: []
180
180
  rubyforge_project: mspire
181
- rubygems_version: 1.8.24
181
+ rubygems_version: 1.8.23
182
182
  signing_key:
183
183
  specification_version: 3
184
184
  summary: An mspire library supporting SEQUEST, Bioworks, SQT, etc