bio-tm_hmm 0.2.1 → 0.2.2

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.
Files changed (10) hide show
  1. data/.travis.yml +1 -1
  2. data/README.md +70 -0
  3. data/Rakefile +5 -0
  4. data/VERSION +1 -1
  5. data/bin/bio-tm_hmm +16 -9
  6. data/bio-tm_hmm.gemspec +6 -5
  7. data/test/test_tm_hmm_parser.rb +57 -0
  8. data/test/test_tm_hmm_wrapper.rb +0 -52
  9. metadata +7 -6
  10. data/README.rdoc +0 -56
data/.travis.yml CHANGED
@@ -9,4 +9,4 @@ rvm:
9
9
  # - rbx-18mode
10
10
 
11
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  # uncomment this line if your project needs to run something other than `rake`:
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- # script: bundle exec rspec spec
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+ script: bundle exec rake test_without_tmhmm
data/README.md ADDED
@@ -0,0 +1,70 @@
1
+ # bio-tm_hmm
2
+
3
+ [![Build Status](https://secure.travis-ci.org/wwood/bioruby-sra.png)](http://travis-ci.org/#!/wwood/bioruby-tm_hmm)
4
+
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+ A bioruby plugin for running the transmembrane domain predictor TMHMM automatically on multiple sequences in a FASTA file and manipulation of the results.
6
+
7
+ ## Installation
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+
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+ ```
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+ gem install bio-tm_hmm
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+ ```
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+
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+ ## Usage
14
+
15
+ ```
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+ Usage: bio-tm_hmm [-f NUM] [-g NUM] [fasta_filename]
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+
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+ fasta file can also be piped in on STDIN.
19
+ without arguments, a description of the transmembrane domains is printed out for each input sequence
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+ -f MIN_TRANSMEMBRANE_DOMAINS, Print those sequences that have at _least_ MIN_TRANSMEMBRANE_DOMAINS transmembrane domain(s). Prints out the sequences in FASTA format.
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+ --filter-in
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+ -g MAX_TRANSMEMBRANE_DOMAINS, Print those sequences that have at _most_ MAX_TRANSMEMBRANE_DOMAINS transmembrane domain(s). Prints out the sequences in FASTA format.
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+ --filter-out
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+ ```
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+
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+ Where my.fasta is a FASTA file with one or more protein sequences in it. Output will be a description of the transmembrane domains predicted by TMHMM.
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+
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+ Other options include -f for printing out the fasta sequences that have some number of transmembrane domains in them, and ignoring those that don't (converse is -g). For instance, to filter out all sequences that have less than 2 predicted transmembrane domains:
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+
30
+ ```
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+ bio-tm_hmm -f 2 <my.fasta
32
+ ```
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+
34
+ ## Developers
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+
36
+ To use the library
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+
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+ ```
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+ require 'bio-tm_hmm'
40
+ ```
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+
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+ The API doc is online. For more code examples see also the test files in
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+ the source tree.
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+
45
+ ## Project home page
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+
47
+ Information on the source tree, documentation, issues and how to contribute, see
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+
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+ http://github.com/wwood/bioruby-tm_hmm
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+
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+ The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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+
53
+ ## Cite
54
+
55
+ If you use this software, please cite:
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+
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+ [Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum](http://genomebiology.com/2012/13/11/R108)
58
+
59
+ Sophie C Oehring, Ben J Woodcroft, Suzette Moes, Johanna Wetzel, Olivier Dietz, Andreas Pulfer, Chaitali Dekiwadia, Pascal Maeser, Christian Flueck, Kathrin Witmer, Nicolas MB Brancucci, Igor Niederwieser, Paul Jenoe, Stuart A Ralph and Till S Voss
60
+
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+ Genome Biology 2012, 13:R108 doi:10.1186/gb-2012-13-11-r108
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+
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+ ## Biogems.info
64
+
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+ This Biogem is published at http://biogems.info/index.html#bio-tm_hmm
66
+
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+ ## Copyright
68
+
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+ Copyright (c) 2012 Ben J Woodcroft. See LICENSE.txt for further details.
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+
data/Rakefile CHANGED
@@ -31,6 +31,11 @@ Rake::TestTask.new(:test) do |test|
31
31
  test.pattern = 'test/**/test_*.rb'
32
32
  test.verbose = true
33
33
  end
34
+ Rake::TestTask.new(:test_without_tmhmm) do |test|
35
+ test.libs << 'lib' << 'test'
36
+ test.test_files = FileList['test/test*.rb'].reject{|f| f=='test/test_tm_hmm_wrapper.rb'}
37
+ test.verbose = true
38
+ end
34
39
 
35
40
  task :default => :test
36
41
 
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.2.1
1
+ 0.2.2
data/bin/bio-tm_hmm CHANGED
@@ -17,16 +17,22 @@ options = {
17
17
  :filter_out => false,
18
18
  }
19
19
  o = OptionParser.new do |opts|
20
- opts.banner = ['',
21
- 'Usage: tm_hmm_wrapper.rb [-fg] [fasta_filename]','',
22
- "\tfasta file can also be piped in on STDIN.",
23
- "\twithout arguments, a description of the transmembranes is printed out for each input sequence",''
24
- ].join("\n")
25
- opts.on('-f','--filter-in [MIN_TRANSMEMBRANE_DOMAINS]','Print those sequences that have a transmembrane domain. If MIN_TRANSMEMBRANE_DOMAINS is defined, only those proteins with that many TMDs or more are printed out') do |m|
20
+ opts.banner = "
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+ Usage: #{File.basename __FILE__} [-f NUM] [-g NUM] [fasta_filename]
22
+
23
+ Fasta file can be piped in on STDIN, or specified as the first unqualified argument.
24
+
25
+ Without arguments, a description of the transmembrane domains is printed out for each input sequence\n\n"
26
+
27
+ opts.on('-f','--filter-in MIN_TRANSMEMBRANE_DOMAINS','Print those sequences that have at _least_ MIN_TRANSMEMBRANE_DOMAINS transmembrane domain(s). Prints out the sequences in FASTA format.') do |m|
26
28
  options[:filter_in] = m.to_i #gets set to 0 when optional MIN_TRANSMEMBRANE_DOMAINS is omitted
27
29
  end
28
- opts.on('-g','--filter-out [MIN_TRANSMEMBRANE_DOMAINS]','Print those sequences that do NOT have a transmembrane domain. If MIN_TRANSMEMBRANE_DOMAINS is defined, only those proteins with that many TMDs or more are filtered out') do |m|
29
- options[:filter_out] = m.to_i #gets set to 0 when optional MIN_TRANSMEMBRANE_DOMAINS is omitted
30
+ opts.on('-g','--filter-out MAX_TRANSMEMBRANE_DOMAINS','Print those sequences that have at _most_ MAX_TRANSMEMBRANE_DOMAINS transmembrane domain(s). Prints out the sequences in FASTA format.') do |m|
31
+ if m.nil?
32
+ options[:filter_out] = 1
33
+ else
34
+ options[:filter_out] = m.to_i
35
+ end
30
36
  end
31
37
  end
32
38
  o.parse!
@@ -39,6 +45,7 @@ Bio::FlatFile.auto(ARGF).each do |seq|
39
45
 
40
46
  # Default output - a description of the TMDs for each input aaseq
41
47
  if options[:filter_in] == false and options[:filter_out] == false
48
+ p result
42
49
  if result.has_domain?
43
50
  # At least one TMD found. Output each on a separate line
44
51
  result.transmembrane_domains.each do |tmd|
@@ -62,7 +69,7 @@ Bio::FlatFile.auto(ARGF).each do |seq|
62
69
  puts seq
63
70
  end
64
71
  elsif options[:filter_out] != false
65
- unless result.transmembrane_domains.length >= options[:filter_out]
72
+ unless result.transmembrane_domains.length > options[:filter_out]
66
73
  puts seq
67
74
  end
68
75
  end
data/bio-tm_hmm.gemspec CHANGED
@@ -5,24 +5,24 @@
5
5
 
6
6
  Gem::Specification.new do |s|
7
7
  s.name = "bio-tm_hmm"
8
- s.version = "0.2.1"
8
+ s.version = "0.2.2"
9
9
 
10
10
  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
11
11
  s.authors = ["Ben J. Woodcroft"]
12
- s.date = "2012-05-03"
12
+ s.date = "2012-12-01"
13
13
  s.description = "A bioruby plugin for interaction with the transmembrane predictor TMHMM"
14
14
  s.email = "donttrustben@gmail.com"
15
15
  s.executables = ["bio-tm_hmm"]
16
16
  s.extra_rdoc_files = [
17
17
  "LICENSE.txt",
18
- "README.rdoc"
18
+ "README.md"
19
19
  ]
20
20
  s.files = [
21
21
  ".document",
22
22
  ".travis.yml",
23
23
  "Gemfile",
24
24
  "LICENSE.txt",
25
- "README.rdoc",
25
+ "README.md",
26
26
  "Rakefile",
27
27
  "VERSION",
28
28
  "bin/bio-tm_hmm",
@@ -32,13 +32,14 @@ Gem::Specification.new do |s|
32
32
  "lib/bio/transmembrane.rb",
33
33
  "test/data/falciparum1.fa",
34
34
  "test/helper.rb",
35
+ "test/test_tm_hmm_parser.rb",
35
36
  "test/test_tm_hmm_wrapper.rb",
36
37
  "test/test_transmembrane.rb"
37
38
  ]
38
39
  s.homepage = "http://github.com/wwood/bioruby-tm_hmm"
39
40
  s.licenses = ["MIT"]
40
41
  s.require_paths = ["lib"]
41
- s.rubygems_version = "1.8.21"
42
+ s.rubygems_version = "1.8.24"
42
43
  s.summary = "A bioruby plugin for interaction with the transmembrane predictor TMHMM"
43
44
 
44
45
  if s.respond_to? :specification_version then
data/test/test_tm_hmm_parser.rb ADDED
@@ -0,0 +1,57 @@
1
+ require 'bio'
2
+ require 'helper'
3
+
4
+ class TmHmmParserTest < Test::Unit::TestCase
5
+ include Bio::Transmembrane
6
+
7
+ def test_parser
8
+ result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0635c len=555 ExpAA=0.00 First60=0.00 PredHel=0 Topology=o')
9
+ assert result
10
+ assert_equal false, result.has_domain?
11
+
12
+ # test a single TMD
13
+ result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0685c len=324 ExpAA=20.36 First60=0.00 PredHel=1 Topology=o281-303i')
14
+ assert result
15
+ assert_equal 1, result.transmembrane_domains.length
16
+ assert_equal 281, result.transmembrane_domains[0].start
17
+ assert_equal 303, result.transmembrane_domains[0].stop
18
+ assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
19
+ result.transmembrane_domains[0].orientation
20
+ assert result.transmembrane_type_1?
21
+ assert_equal false, result.transmembrane_type_2?
22
+
23
+ # test 2 TMD
24
+ result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0680c len=209 ExpAA=43.03 First60=0.02 PredHel=2 Topology=i137-159o164-183i')
25
+ assert result
26
+ assert_equal 2, result.transmembrane_domains.length
27
+ assert_equal 137, result.transmembrane_domains[0].start
28
+ assert_equal 159, result.transmembrane_domains[0].stop
29
+ assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::INSIDE_OUT,
30
+ result.transmembrane_domains[0].orientation
31
+ assert_equal 164, result.transmembrane_domains[1].start
32
+ assert_equal 183, result.transmembrane_domains[1].stop
33
+ assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
34
+ result.transmembrane_domains[1].orientation
35
+ assert_equal false, result.transmembrane_type_1?
36
+ assert_equal false, result.transmembrane_type_2?
37
+
38
+ # test 3 TMD
39
+ result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0705c len=282 ExpAA=90.97 First60=22.20 PredHel=4 Topology=i22-44o185-207i212-234o259-281i')
40
+ assert result
41
+ assert_equal 4, result.transmembrane_domains.length
42
+ assert_equal 22, result.transmembrane_domains[0].start
43
+ assert_equal 44, result.transmembrane_domains[0].stop
44
+ assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::INSIDE_OUT,
45
+ result.transmembrane_domains[0].orientation
46
+ assert_equal 185, result.transmembrane_domains[1].start
47
+ assert_equal 207, result.transmembrane_domains[1].stop
48
+ assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
49
+ result.transmembrane_domains[1].orientation
50
+ assert_equal 259, result.transmembrane_domains[3].start
51
+ assert_equal 281, result.transmembrane_domains[3].stop
52
+ assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
53
+ result.transmembrane_domains[3].orientation
54
+ assert_equal false, result.transmembrane_type_1?
55
+ assert_equal false, result.transmembrane_type_2?
56
+ end
57
+ end
data/test/test_tm_hmm_wrapper.rb CHANGED
@@ -3,58 +3,6 @@ require 'helper'
3
3
 
4
4
  class TmHmmWrapperTest < Test::Unit::TestCase
5
5
  include Bio::Transmembrane
6
-
7
- def test_parser
8
- result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0635c len=555 ExpAA=0.00 First60=0.00 PredHel=0 Topology=o')
9
- assert result
10
- assert_equal false, result.has_domain?
11
-
12
- # test a single TMD
13
- result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0685c len=324 ExpAA=20.36 First60=0.00 PredHel=1 Topology=o281-303i')
14
- assert result
15
- assert_equal 1, result.transmembrane_domains.length
16
- assert_equal 281, result.transmembrane_domains[0].start
17
- assert_equal 303, result.transmembrane_domains[0].stop
18
- assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
19
- result.transmembrane_domains[0].orientation
20
- assert result.transmembrane_type_1?
21
- assert_equal false, result.transmembrane_type_2?
22
-
23
- # test 2 TMD
24
- result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0680c len=209 ExpAA=43.03 First60=0.02 PredHel=2 Topology=i137-159o164-183i')
25
- assert result
26
- assert_equal 2, result.transmembrane_domains.length
27
- assert_equal 137, result.transmembrane_domains[0].start
28
- assert_equal 159, result.transmembrane_domains[0].stop
29
- assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::INSIDE_OUT,
30
- result.transmembrane_domains[0].orientation
31
- assert_equal 164, result.transmembrane_domains[1].start
32
- assert_equal 183, result.transmembrane_domains[1].stop
33
- assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
34
- result.transmembrane_domains[1].orientation
35
- assert_equal false, result.transmembrane_type_1?
36
- assert_equal false, result.transmembrane_type_2?
37
-
38
- # test 3 TMD
39
- result = Bio::TMHMM::TmHmmResult.create_from_short_line('PFA0705c len=282 ExpAA=90.97 First60=22.20 PredHel=4 Topology=i22-44o185-207i212-234o259-281i')
40
- assert result
41
- assert_equal 4, result.transmembrane_domains.length
42
- assert_equal 22, result.transmembrane_domains[0].start
43
- assert_equal 44, result.transmembrane_domains[0].stop
44
- assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::INSIDE_OUT,
45
- result.transmembrane_domains[0].orientation
46
- assert_equal 185, result.transmembrane_domains[1].start
47
- assert_equal 207, result.transmembrane_domains[1].stop
48
- assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
49
- result.transmembrane_domains[1].orientation
50
- assert_equal 259, result.transmembrane_domains[3].start
51
- assert_equal 281, result.transmembrane_domains[3].stop
52
- assert_equal Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN,
53
- result.transmembrane_domains[3].orientation
54
- assert_equal false, result.transmembrane_type_1?
55
- assert_equal false, result.transmembrane_type_2?
56
- end
57
-
58
6
  def test_wrapper
59
7
  prog = Bio::TMHMM::TmHmmWrapper.new
60
8
  seq = Bio::FlatFile.auto(File.join(File.dirname(__FILE__),'data','falciparum1.fa')).next_entry
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bio-tm_hmm
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.2.1
4
+ version: 0.2.2
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: 2012-05-03 00:00:00.000000000 Z
12
+ date: 2012-12-01 00:00:00.000000000 Z
13
13
  dependencies:
14
14
  - !ruby/object:Gem::Dependency
15
15
  name: shoulda
@@ -98,13 +98,13 @@ executables:
98
98
  extensions: []
99
99
  extra_rdoc_files:
100
100
  - LICENSE.txt
101
- - README.rdoc
101
+ - README.md
102
102
  files:
103
103
  - .document
104
104
  - .travis.yml
105
105
  - Gemfile
106
106
  - LICENSE.txt
107
- - README.rdoc
107
+ - README.md
108
108
  - Rakefile
109
109
  - VERSION
110
110
  - bin/bio-tm_hmm
@@ -114,6 +114,7 @@ files:
114
114
  - lib/bio/transmembrane.rb
115
115
  - test/data/falciparum1.fa
116
116
  - test/helper.rb
117
+ - test/test_tm_hmm_parser.rb
117
118
  - test/test_tm_hmm_wrapper.rb
118
119
  - test/test_transmembrane.rb
119
120
  homepage: http://github.com/wwood/bioruby-tm_hmm
@@ -131,7 +132,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
131
132
  version: '0'
132
133
  segments:
133
134
  - 0
134
- hash: 1004564205
135
+ hash: 24340783
135
136
  required_rubygems_version: !ruby/object:Gem::Requirement
136
137
  none: false
137
138
  requirements:
@@ -140,7 +141,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
140
141
  version: '0'
141
142
  requirements: []
142
143
  rubyforge_project:
143
- rubygems_version: 1.8.21
144
+ rubygems_version: 1.8.24
144
145
  signing_key:
145
146
  specification_version: 3
146
147
  summary: A bioruby plugin for interaction with the transmembrane predictor TMHMM
data/README.rdoc DELETED
@@ -1,56 +0,0 @@
1
- = bio-tm_hmm
2
-
3
- {<img
4
- src="https://secure.travis-ci.org/wwood/bioruby-tm_hmm.png"
5
- />}[http://travis-ci.org/#!/wwood/bioruby-tm_hmm]
6
-
7
- A bioruby plugin for running TMHMM automatically on multiple sequences in a FASTA file and manipulation of the results
8
-
9
- Note: this software is under active development!
10
-
11
- == Installation
12
-
13
- gem install bio-tm_hmm
14
-
15
- == Usage
16
-
17
- bio-tm_hmm my.fasta
18
-
19
- Where my.fasta is a FASTA file with one or more protein sequences in it. Output will be a description of the transmembrane domains predicted by TMHMM.
20
-
21
- Other options include -f for printing out the fasta sequences that have some number of transmembrane domains in them, and ignoring those that done (converse is -g)
22
-
23
- bio-tm_hmm -f 2 <my.fasta
24
-
25
- == Developers
26
-
27
- To use the library
28
-
29
- require 'bio-tm_hmm'
30
-
31
- The API doc is online. For more code examples see also the test files in
32
- the source tree.
33
-
34
- == Project home page
35
-
36
- Information on the source tree, documentation, issues and how to contribute, see
37
-
38
- http://github.com/wwood/bioruby-tm_hmm
39
-
40
- The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
41
-
42
- == Cite
43
-
44
- If you use this software, please cite one of
45
-
46
- * [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
47
- * [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
48
-
49
- == Biogems.info
50
-
51
- This Biogem is published at http://biogems.info/index.html#bio-tm_hmm
52
-
53
- == Copyright
54
-
55
- Copyright (c) 2012 Ben J Woodcroft. See LICENSE.txt for further details.
56
-