protk 1.2.6.pre1 → 1.2.6.pre2

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.
@@ -19,6 +19,11 @@ include LibXML
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  tool=Tool.new([:explicit_output])
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  tool.option_parser.banner = "Convert a protXML file to a tab delimited table.\n\nUsage: protxml_to_table.rb [options] file1.protXML"
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+ tool.options.groups=false
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+ tool.option_parser.on("--groups","Print output by groups rather than for each protein") do
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+ tool.options.groups=true
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+ end
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+
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  # tool.options.proteinid_regex=".*?\|.*?\|(.*)"
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  # tool.option_parser.on( '--regex rexpr', 'Regex' ) do |regex|
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  # tool.options.proteinid_regex=regex
@@ -58,8 +63,10 @@ column_headers=[
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  "num_peptides","confidence"
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  ]
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- output_fh.write "#{column_headers.join("\t")}\n"
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+ groups_column_headers=["group_number","group_probability","members"]
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+ output_fh.write "#{column_headers.join("\t")}\n" unless tool.groups
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+ output_fh.write "#{groups_column_headers.join("\t")}\n" if tool.groups
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70
 
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  protein_groups=protxml_doc.find("//#{protxml_ns_prefix}protein_group", protxml_ns)
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@@ -67,6 +74,8 @@ protein_groups.each do |protein_group|
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  proteins=protein_group.find("./#{protxml_ns_prefix}protein", protxml_ns)
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+ group_members=[]
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+
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  proteins.each do |protein|
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  indis_proteins=protein.find("./#{protxml_ns_prefix}indistinguishable_protein", protxml_ns)
@@ -78,6 +87,8 @@ protein_groups.each do |protein_group|
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  protein_id=protein.attributes['protein_name'].match(/.*?\|.*?\|(.*)/)[1]
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  end
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+ group_members<<protein.attributes['protein_name']
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+
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  column_values=[]
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  column_values << protein_group.attributes['group_number']
@@ -91,9 +102,21 @@ protein_groups.each do |protein_group|
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  column_values << protein.attributes['unique_stripped_peptides']
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  column_values << protein.attributes['total_number_peptides']
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  column_values << protein.attributes['confidence']
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- output_fh.write(column_values.join("\t"))
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- output_fh.write("\n")
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105
 
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+ unless tool.groups
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+ output_fh.write(column_values.join("\t"))
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+ output_fh.write("\n")
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+ end
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  end
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+
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+ group_column_values=[protein_group.attributes['group_number']]
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+ group_column_values<<protein_group.attributes['probability']
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+ group_column_values<<group_members.join(" ")
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+
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+ if tool.groups
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+ output_fh.write(group_column_values.join("\t"))
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+ output_fh.write("\n")
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+ end
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+
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  end
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data/bin/tandem_search.rb CHANGED
@@ -22,7 +22,7 @@ genv=Constants.new
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  #
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  search_tool=SearchTool.new([:background,:glyco,:database,:explicit_output,:over_write,
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  :enzyme,:modifications,:mass_tolerance_units,:mass_tolerance,:strict_monoisotopic_mass,
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- :missed_cleavages,:carbamidomethyl,:methionine_oxidation
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+ :missed_cleavages,:cleavage_semi,:carbamidomethyl,:methionine_oxidation
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  ])
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  search_tool.jobid_prefix="x"
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  search_tool.option_parser.banner = "Run an X!Tandem msms search on a set of mzML input files.\n\nUsage: tandem_search.rb [options] file1.mzML file2.mzML ..."
@@ -133,7 +133,7 @@ class Constants
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  end
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134
 
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  def msgfplusjar
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- return "#{self.msgfplus_root}/MSGFPlus.jar"
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+ return %x[which MSGFPlus.jar]
137
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  end
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138
 
139
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  def pwiz_root
@@ -236,7 +236,7 @@ class Constants
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  @protk_dir=ENV['PROTK_INSTALL_DIR']
237
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  end
238
238
 
239
- # Protk Defaults
239
+ # Load Protk Defaults
240
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  #
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  default_config_yml = YAML.load_file "#{File.dirname(__FILE__)}/data/default_config.yml"
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  throw "Unable to read the config file at #{File.dirname(__FILE__)}/data/default_config.yml" unless default_config_yml!=nil
@@ -251,31 +251,31 @@ class Constants
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  @env=default_config_yml
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252
  end
253
253
 
254
- # Application installation directories. From environment variables
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+ protk_tool_dirs=["tpp","omssa","openms","msgfplus","blast","pwiz","tandem"]
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+
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+ # Construct the PATH variable by prepending our preferred paths
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  #
256
- protk_roots = [["tpp","xinteract"],["omssa","omssacl"],["blast","blastdbcmd"],["pwiz","msconvert"],["msgfplus",""],["openms","ExecutePipeline"]]
258
+ protk_paths=[]
257
259
 
258
- protk_roots.each do |r,binaryname|
259
- env_value = ENV["PROTK_#{r.upcase}_ROOT"]
260
+ # Add PATHs if PROTK_XXX_ROOT is defined
261
+ #
262
+ protk_tool_dirs.each do |tooldir|
263
+ env_value = ENV["PROTK_#{tooldir.upcase}_ROOT"]
260
264
  if ( env_value!=nil)
261
- # "FROMPATH" means detect the root value
262
- if env_value=="FROMPATH"
263
- bin_path=Pathname.new(%x[which #{binaryname}].chomp)
264
- if bin_path.exist?
265
- env_value=bin_path.realpath.dirname.to_s
266
- else
267
- env_value=""
268
- end
269
- end
270
- p "Using #{r} root #{env_value}"
271
- @env["#{r}_root"]=env_value
265
+ protk_paths<<env_value
272
266
  end
267
+ protk_paths<<"#{@protk_dir}/tools/#{tooldir}"
273
268
  end
269
+
270
+ original_path=ENV['PATH']
271
+ protk_paths<<original_path
272
+
273
+
274
+ ENV['PATH']=protk_paths.join(":")
275
+
274
276
 
275
277
  throw "No data found in config file" unless @env!=nil
276
278
  @info_level=default_config_yml['message_level']
277
-
278
-
279
279
 
280
280
  end
281
281
 
@@ -12,11 +12,4 @@ uniprot_sprot_annotation_database: swissprot_annotation
12
12
  uniprot_trembl_annotation_database: trembl_annotation
13
13
  galaxy_root: galaxy
14
14
  default_mascot_server: www.matrixscience.com
15
- tpp_root: tools/tpp
16
- omssa_root: tools/omssa
17
- openms_root: tools/openms
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- msgfplus_root: tools/msgfplus
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- blast_root: tools/blast
20
- pwiz_root: tools/pwiz
21
- tandem_root: tools/tandem
22
15
  log_file: Logs/protk.log
@@ -100,6 +100,13 @@ class SearchTool < Tool
100
100
  end
101
101
  end
102
102
 
103
+ if ( option_support.include? :cleavage_semi )
104
+ @options.cleavage_semi=true
105
+ @option_parser.on( '--no-cleavage-semi', 'Dont allow up to 1 non tryptic terminus on peptides' ) do
106
+ @options.cleavage_semi=false
107
+ end
108
+ end
109
+
103
110
  if ( option_support.include? :respect_precursor_charges )
104
111
  @options.respect_precursor_charges=false
105
112
  @option_parser.on( '-q', '--respect-charges','Dont respect charges in the input file. Instead impute them by trying various options') do
metadata CHANGED
@@ -1,8 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
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2
  name: protk
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.2.6.pre1
5
- prerelease: 6
4
+ version: 1.2.6.pre2
6
5
  platform: ruby
7
6
  authors:
8
7
  - Ira Cooke
@@ -14,151 +13,186 @@ dependencies:
14
13
  - !ruby/object:Gem::Dependency
15
14
  name: ftools
16
15
  requirement: !ruby/object:Gem::Requirement
17
- none: false
18
16
  requirements:
19
- - - ! '>='
17
+ - - ~>
18
+ - !ruby/object:Gem::Version
19
+ version: '0.0'
20
+ - - '>='
20
21
  - !ruby/object:Gem::Version
21
22
  version: 0.0.0
22
23
  type: :runtime
23
24
  prerelease: false
24
25
  version_requirements: !ruby/object:Gem::Requirement
25
- none: false
26
26
  requirements:
27
- - - ! '>='
27
+ - - ~>
28
+ - !ruby/object:Gem::Version
29
+ version: '0.0'
30
+ - - '>='
28
31
  - !ruby/object:Gem::Version
29
32
  version: 0.0.0
30
33
  - !ruby/object:Gem::Dependency
31
34
  name: open4
32
35
  requirement: !ruby/object:Gem::Requirement
33
- none: false
34
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  requirements:
35
- - - ! '>='
37
+ - - ~>
38
+ - !ruby/object:Gem::Version
39
+ version: '1.3'
40
+ - - '>='
36
41
  - !ruby/object:Gem::Version
37
42
  version: 1.3.0
38
43
  type: :runtime
39
44
  prerelease: false
40
45
  version_requirements: !ruby/object:Gem::Requirement
41
- none: false
42
46
  requirements:
43
- - - ! '>='
47
+ - - ~>
48
+ - !ruby/object:Gem::Version
49
+ version: '1.3'
50
+ - - '>='
44
51
  - !ruby/object:Gem::Version
45
52
  version: 1.3.0
46
53
  - !ruby/object:Gem::Dependency
47
54
  name: bio
48
55
  requirement: !ruby/object:Gem::Requirement
49
- none: false
50
56
  requirements:
51
- - - ! '>='
57
+ - - ~>
58
+ - !ruby/object:Gem::Version
59
+ version: '1.4'
60
+ - - '>='
52
61
  - !ruby/object:Gem::Version
53
62
  version: 1.4.3
54
63
  type: :runtime
55
64
  prerelease: false
56
65
  version_requirements: !ruby/object:Gem::Requirement
57
- none: false
58
66
  requirements:
59
- - - ! '>='
67
+ - - ~>
68
+ - !ruby/object:Gem::Version
69
+ version: '1.4'
70
+ - - '>='
60
71
  - !ruby/object:Gem::Version
61
72
  version: 1.4.3
62
73
  - !ruby/object:Gem::Dependency
63
74
  name: rest-client
64
75
  requirement: !ruby/object:Gem::Requirement
65
- none: false
66
76
  requirements:
67
- - - ! '>='
77
+ - - ~>
78
+ - !ruby/object:Gem::Version
79
+ version: 1.6.7
80
+ - - '>='
68
81
  - !ruby/object:Gem::Version
69
82
  version: 1.6.7
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83
  type: :runtime
71
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  prerelease: false
72
85
  version_requirements: !ruby/object:Gem::Requirement
73
- none: false
74
86
  requirements:
75
- - - ! '>='
87
+ - - ~>
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+ - !ruby/object:Gem::Version
89
+ version: 1.6.7
90
+ - - '>='
76
91
  - !ruby/object:Gem::Version
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92
  version: 1.6.7
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93
  - !ruby/object:Gem::Dependency
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  name: net-ftp-list
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95
  requirement: !ruby/object:Gem::Requirement
81
- none: false
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  requirements:
83
- - - ! '>='
97
+ - - ~>
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+ - !ruby/object:Gem::Version
99
+ version: 3.2.5
100
+ - - '>='
84
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  - !ruby/object:Gem::Version
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102
  version: 3.2.5
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103
  type: :runtime
87
104
  prerelease: false
88
105
  version_requirements: !ruby/object:Gem::Requirement
89
- none: false
90
106
  requirements:
91
- - - ! '>='
107
+ - - ~>
108
+ - !ruby/object:Gem::Version
109
+ version: 3.2.5
110
+ - - '>='
92
111
  - !ruby/object:Gem::Version
93
112
  version: 3.2.5
94
113
  - !ruby/object:Gem::Dependency
95
114
  name: spreadsheet
96
115
  requirement: !ruby/object:Gem::Requirement
97
- none: false
98
116
  requirements:
99
- - - ! '>='
117
+ - - ~>
118
+ - !ruby/object:Gem::Version
119
+ version: 0.7.4
120
+ - - '>='
100
121
  - !ruby/object:Gem::Version
101
122
  version: 0.7.4
102
123
  type: :runtime
103
124
  prerelease: false
104
125
  version_requirements: !ruby/object:Gem::Requirement
105
- none: false
106
126
  requirements:
107
- - - ! '>='
127
+ - - ~>
128
+ - !ruby/object:Gem::Version
129
+ version: 0.7.4
130
+ - - '>='
108
131
  - !ruby/object:Gem::Version
109
132
  version: 0.7.4
110
133
  - !ruby/object:Gem::Dependency
111
134
  name: libxml-ruby
112
135
  requirement: !ruby/object:Gem::Requirement
113
- none: false
114
136
  requirements:
115
- - - ! '>='
137
+ - - ~>
116
138
  - !ruby/object:Gem::Version
117
- version: 2.3.3
139
+ version: '2.7'
140
+ - - '>='
141
+ - !ruby/object:Gem::Version
142
+ version: 2.7.0
118
143
  type: :runtime
119
144
  prerelease: false
120
145
  version_requirements: !ruby/object:Gem::Requirement
121
- none: false
122
146
  requirements:
123
- - - ! '>='
147
+ - - ~>
124
148
  - !ruby/object:Gem::Version
125
- version: 2.3.3
149
+ version: '2.7'
150
+ - - '>='
151
+ - !ruby/object:Gem::Version
152
+ version: 2.7.0
126
153
  - !ruby/object:Gem::Dependency
127
154
  name: mascot-dat
128
155
  requirement: !ruby/object:Gem::Requirement
129
- none: false
130
156
  requirements:
131
- - - ! '>='
157
+ - - ~>
158
+ - !ruby/object:Gem::Version
159
+ version: 0.3.1
160
+ - - '>='
132
161
  - !ruby/object:Gem::Version
133
162
  version: 0.3.1
134
163
  type: :runtime
135
164
  prerelease: false
136
165
  version_requirements: !ruby/object:Gem::Requirement
137
- none: false
138
166
  requirements:
139
- - - ! '>='
167
+ - - ~>
168
+ - !ruby/object:Gem::Version
169
+ version: 0.3.1
170
+ - - '>='
140
171
  - !ruby/object:Gem::Version
141
172
  version: 0.3.1
142
173
  - !ruby/object:Gem::Dependency
143
174
  name: bio-blastxmlparser
144
175
  requirement: !ruby/object:Gem::Requirement
145
- none: false
146
176
  requirements:
147
- - - ! '>='
177
+ - - ~>
178
+ - !ruby/object:Gem::Version
179
+ version: 1.1.1
180
+ - - '>='
148
181
  - !ruby/object:Gem::Version
149
182
  version: 1.1.1
150
183
  type: :runtime
151
184
  prerelease: false
152
185
  version_requirements: !ruby/object:Gem::Requirement
153
- none: false
154
186
  requirements:
155
- - - ! '>='
187
+ - - ~>
188
+ - !ruby/object:Gem::Version
189
+ version: 1.1.1
190
+ - - '>='
156
191
  - !ruby/object:Gem::Version
157
192
  version: 1.1.1
158
193
  - !ruby/object:Gem::Dependency
159
194
  name: rspec
160
195
  requirement: !ruby/object:Gem::Requirement
161
- none: false
162
196
  requirements:
163
197
  - - ~>
164
198
  - !ruby/object:Gem::Version
@@ -166,7 +200,6 @@ dependencies:
166
200
  type: :development
167
201
  prerelease: false
168
202
  version_requirements: !ruby/object:Gem::Requirement
169
- none: false
170
203
  requirements:
171
204
  - - ~>
172
205
  - !ruby/object:Gem::Version
@@ -211,37 +244,7 @@ extensions:
211
244
  - ext/protk/decoymaker/extconf.rb
212
245
  extra_rdoc_files: []
213
246
  files:
214
- - lib/protk/bio_sptr_extensions.rb
215
- - lib/protk/biotools_excel_converter.rb
216
- - lib/protk/command_runner.rb
217
- - lib/protk/constants.rb
218
- - lib/protk/convert_util.rb
219
- - lib/protk/data/make_uniprot_table.rb
220
- - lib/protk/eupathdb_gene_information_table.rb
221
- - lib/protk/fastadb.rb
222
- - lib/protk/galaxy_stager.rb
223
- - lib/protk/galaxy_util.rb
224
- - lib/protk/gapped_aligner.rb
225
- - lib/protk/manage_db_tool.rb
226
- - lib/protk/mascot_util.rb
227
- - lib/protk/omssa_util.rb
228
- - lib/protk/openms_defaults.rb
229
- - lib/protk/pepxml.rb
230
- - lib/protk/plasmodb.rb
231
- - lib/protk/prophet_tool.rb
232
- - lib/protk/protein_annotator.rb
233
- - lib/protk/protxml.rb
234
- - lib/protk/randomize.rb
235
- - lib/protk/search_tool.rb
236
- - lib/protk/setup_tool.rb
237
- - lib/protk/spreadsheet_extensions.rb
238
- - lib/protk/swissprot_database.rb
239
- - lib/protk/tool.rb
240
- - lib/protk/uniprot_mapper.rb
241
- - lib/protk/xtandem_defaults.rb
242
- - lib/protk.rb
243
- - lib/protk/manage_db_rakefile.rake
244
- - lib/protk/setup_rakefile.rake
247
+ - README.md
245
248
  - bin/add_retention_times.rb
246
249
  - bin/annotate_ids.rb
247
250
  - bin/asapratio.rb
@@ -256,7 +259,6 @@ files:
256
259
  - bin/libra.rb
257
260
  - bin/make_decoy.rb
258
261
  - bin/manage_db.rb
259
- - bin/mascot2xml.rb
260
262
  - bin/mascot_search.rb
261
263
  - bin/mascot_to_pepxml.rb
262
264
  - bin/msgfplus_search.rb
@@ -276,20 +278,27 @@ files:
276
278
  - bin/uniprot_mapper.rb
277
279
  - bin/xls_to_table.rb
278
280
  - bin/xpress.rb
279
- - README.md
280
- - lib/protk/data/apt-get_packages.yaml
281
- - lib/protk/data/brew_packages.yaml
282
- - lib/protk/data/default_config.yml
281
+ - ext/protk/decoymaker/decoymaker.c
282
+ - ext/protk/decoymaker/extconf.rb
283
+ - ext/protk/simplealign/extconf.rb
284
+ - lib/protk.rb
285
+ - lib/protk/bio_sptr_extensions.rb
286
+ - lib/protk/biotools_excel_converter.rb
287
+ - lib/protk/command_runner.rb
288
+ - lib/protk/constants.rb
289
+ - lib/protk/convert_util.rb
283
290
  - lib/protk/data/ExecutePipeline.trf
284
291
  - lib/protk/data/FeatureFinderCentroided.ini
285
292
  - lib/protk/data/FeatureFinderIsotopeWavelet.ini
293
+ - lib/protk/data/apt-get_packages.yaml
294
+ - lib/protk/data/brew_packages.yaml
295
+ - lib/protk/data/default_config.yml
286
296
  - lib/protk/data/galaxyenv.sh
287
- - lib/protk/data/pepxml_mascot_template.xml
297
+ - lib/protk/data/make_uniprot_table.rb
288
298
  - lib/protk/data/predefined_db.crap.yaml
289
299
  - lib/protk/data/predefined_db.sphuman.yaml
290
300
  - lib/protk/data/predefined_db.swissprot_annotation.yaml
291
301
  - lib/protk/data/predefined_db.swissprot_fasta_annotation.yaml
292
- - lib/protk/data/predefined_db.trembl_annotation.yaml
293
302
  - lib/protk/data/tandem_params.xml
294
303
  - lib/protk/data/taxonomy_template.xml
295
304
  - lib/protk/data/unimod.xml
@@ -297,34 +306,53 @@ files:
297
306
  - lib/protk/data/uniprot_accessions_table.txt
298
307
  - lib/protk/data/uniprot_input_accessions.loc
299
308
  - lib/protk/data/yum_packages.yaml
300
- - ext/protk/decoymaker/decoymaker.c
301
- - ext/protk/simplealign/simplealign.c
302
- - ext/protk/decoymaker/extconf.rb
303
- - ext/protk/simplealign/extconf.rb
309
+ - lib/protk/eupathdb_gene_information_table.rb
310
+ - lib/protk/fastadb.rb
311
+ - lib/protk/galaxy_stager.rb
312
+ - lib/protk/galaxy_util.rb
313
+ - lib/protk/gapped_aligner.rb
314
+ - lib/protk/manage_db_rakefile.rake
315
+ - lib/protk/manage_db_tool.rb
316
+ - lib/protk/mascot_util.rb
317
+ - lib/protk/omssa_util.rb
318
+ - lib/protk/openms_defaults.rb
319
+ - lib/protk/pepxml.rb
320
+ - lib/protk/plasmodb.rb
321
+ - lib/protk/prophet_tool.rb
322
+ - lib/protk/protein_annotator.rb
323
+ - lib/protk/protxml.rb
324
+ - lib/protk/randomize.rb
325
+ - lib/protk/search_tool.rb
326
+ - lib/protk/setup_rakefile.rake
327
+ - lib/protk/setup_tool.rb
328
+ - lib/protk/spreadsheet_extensions.rb
329
+ - lib/protk/swissprot_database.rb
330
+ - lib/protk/tool.rb
331
+ - lib/protk/uniprot_mapper.rb
332
+ - lib/protk/xtandem_defaults.rb
304
333
  homepage: http://rubygems.org/gems/protk
305
334
  licenses: []
335
+ metadata: {}
306
336
  post_install_message: Now run protk_setup.rb to install third party tools and manage_db.rb
307
337
  to install databases.
308
338
  rdoc_options: []
309
339
  require_paths:
310
340
  - lib
311
341
  required_ruby_version: !ruby/object:Gem::Requirement
312
- none: false
313
342
  requirements:
314
- - - ! '>='
343
+ - - '>='
315
344
  - !ruby/object:Gem::Version
316
345
  version: '0'
317
346
  required_rubygems_version: !ruby/object:Gem::Requirement
318
- none: false
319
347
  requirements:
320
- - - ! '>'
348
+ - - '>'
321
349
  - !ruby/object:Gem::Version
322
350
  version: 1.3.1
323
351
  requirements: []
324
352
  rubyforge_project:
325
- rubygems_version: 1.8.24
353
+ rubygems_version: 2.2.1
326
354
  signing_key:
327
- specification_version: 3
355
+ specification_version: 4
328
356
  summary: Proteomics Toolkit
329
357
  test_files: []
330
358
  has_rdoc: