transrate 0.1.0 → 0.2.0
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- checksums.yaml +4 -4
- data/.gitignore +16 -1
- data/.travis.yml +8 -0
- data/README.md +45 -43
- data/Rakefile +36 -0
- data/bin/transrate +98 -50
- data/deps/deps.yaml +55 -0
- data/lib/transrate.rb +19 -4
- data/lib/transrate/assembly.rb +93 -182
- data/lib/transrate/bowtie2.rb +37 -13
- data/lib/transrate/cmd.rb +19 -0
- data/lib/transrate/comparative_metrics.rb +239 -19
- data/lib/transrate/contig.rb +212 -0
- data/lib/transrate/contig_metrics.rb +76 -0
- data/lib/transrate/read_metrics.rb +83 -41
- data/lib/transrate/samtools.rb +73 -0
- data/lib/transrate/transrater.rb +31 -11
- data/lib/transrate/version.rb +1 -1
- data/test/data/150uncovered.l.fq +892 -0
- data/test/data/150uncovered.r.fq +892 -0
- data/test/data/Os.protein.2.fa +95 -0
- data/test/data/Os.protein.fa +199 -0
- data/test/data/assembly.2.fa +26 -0
- data/test/{assembly.fasta → data/assembly.fasta} +0 -0
- data/test/data/bridging_reads.l.fastq +20 -0
- data/test/data/bridging_reads.r.fastq +20 -0
- data/test/data/sorghum_transcript.fa +4 -0
- data/test/data/tiny.sam +4 -0
- data/test/helper.rb +33 -2
- data/test/test_bowtie.rb +54 -0
- data/test/test_cmd.rb +15 -0
- data/test/test_comp_metrics.rb +177 -0
- data/test/test_contig.rb +61 -0
- data/test/test_contig_metrics.rb +50 -0
- data/test/test_inline.rb +10 -9
- data/test/test_read_metrics.rb +68 -0
- data/test/test_samtools.rb +22 -0
- data/test/test_transrate.rb +40 -0
- data/test/test_transrater.rb +68 -0
- data/transrate.gemspec +16 -10
- metadata +232 -57
- data/lib/transrate/express.rb +0 -37
- data/lib/transrate/log.rb +0 -16
- data/lib/transrate/rb_hit.rb +0 -33
- data/lib/transrate/reciprocal_annotation.rb +0 -105
- data/lib/transrate/usearch.rb +0 -66
- data/test/test_test.rb +0 -41
@@ -0,0 +1,68 @@
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1
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+
#!/usr/bin/env ruby
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2
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3
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+
require 'helper'
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4
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+
require 'tmpdir'
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5
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+
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6
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+
class TestTransrater < Test::Unit::TestCase
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7
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+
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8
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+
context "transrater" do
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9
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+
|
10
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+
setup do
|
11
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+
@assembly = File.join(File.dirname(__FILE__), 'data', 'assembly.2.fa')
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12
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+
@reference = File.join(File.dirname(__FILE__), 'data', 'Os.protein.2.fa')
|
13
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+
@rater = Transrate::Transrater.new(@assembly, @reference)
|
14
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+
@left = File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
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15
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+
@right = File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
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16
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+
end
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17
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+
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18
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should "create transrater object" do
|
19
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assert @rater
|
20
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+
end
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21
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+
|
22
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+
should "raise error when assembly input is nil" do
|
23
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assert_raise RuntimeError do
|
24
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+
rater = Transrate::Transrater.new(nil, @reference)
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25
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+
end
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26
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end
|
27
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+
|
28
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should "handle assembly as an assemby object" do
|
29
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assembly_object = Transrate::Assembly.new(@assembly)
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30
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+
rater = Transrate::Transrater.new(assembly_object, @reference)
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31
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end
|
32
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+
|
33
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should "handle reference as an assemby object" do
|
34
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reference_object = Transrate::Assembly.new(@reference)
|
35
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+
rater = Transrate::Transrater.new(@assembly, reference_object)
|
36
|
+
end
|
37
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+
|
38
|
+
should "run assembly metrics without input fastq files" do
|
39
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Dir.mktmpdir do |tmpdir|
|
40
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+
Dir.chdir tmpdir do
|
41
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+
stats = @rater.assembly_metrics
|
42
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+
assert_equal 1566, stats.n50
|
43
|
+
assert_equal 10331, stats.n_bases
|
44
|
+
end
|
45
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+
end
|
46
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+
end
|
47
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+
|
48
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+
should "run read metrics with input fastq files" do
|
49
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Dir.mktmpdir do |tmpdir|
|
50
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+
Dir.chdir tmpdir do
|
51
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+
stats = @rater.read_metrics(@left, @right)
|
52
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+
assert_equal 223, stats.read_stats[:num_pairs]
|
53
|
+
end
|
54
|
+
end
|
55
|
+
end
|
56
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+
|
57
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+
should "get assembly score" do
|
58
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+
Dir.mktmpdir do |tmpdir|
|
59
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+
Dir.chdir tmpdir do
|
60
|
+
all = @rater.all_metrics(@left, @right)
|
61
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+
score = @rater.assembly_score
|
62
|
+
assert_equal 0.23282, score.round(5)
|
63
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+
end
|
64
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+
end
|
65
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+
end
|
66
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+
|
67
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end
|
68
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end
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data/transrate.gemspec
CHANGED
@@ -4,7 +4,7 @@ require File.expand_path('../lib/transrate/version', __FILE__)
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|
4
4
|
|
5
5
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Gem::Specification.new do |gem|
|
6
6
|
gem.name = 'transrate'
|
7
|
-
gem.authors = [ "Richard Smith" ]
|
7
|
+
gem.authors = [ "Richard Smith-Unna", "Chris Boursnell" ]
|
8
8
|
gem.email = "rds45@cam.ac.uk"
|
9
9
|
gem.licenses = ["MIT"]
|
10
10
|
gem.homepage = 'https://github.com/Blahah/transrate'
|
@@ -16,15 +16,21 @@ Gem::Specification.new do |gem|
|
|
16
16
|
gem.executables = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
|
17
17
|
gem.require_paths = %w( lib )
|
18
18
|
|
19
|
-
gem.add_dependency '
|
20
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-
gem.add_dependency 'trollop'
|
21
|
-
gem.add_dependency '
|
22
|
-
gem.add_dependency '
|
23
|
-
gem.add_dependency '
|
19
|
+
gem.add_dependency 'yell', '~> 2.0', '>= 2.0.4'
|
20
|
+
gem.add_dependency 'trollop', '~> 2.0'
|
21
|
+
gem.add_dependency 'bindeps', '~> 0.0', '>= 0.0.7'
|
22
|
+
gem.add_dependency 'which', '~> 0.0', '>= 0.0.2'
|
23
|
+
gem.add_dependency 'bio', '~> 1.4', '>= 1.4.3'
|
24
|
+
gem.add_dependency 'bio-samtools', '~> 2.0', '>= 2.0.5'
|
24
25
|
gem.add_dependency 'RubyInline', '~> 3.12'
|
26
|
+
gem.add_dependency 'crb-blast', '~> 0.2'
|
27
|
+
gem.add_dependency 'bettersam', '~> 0.0', '>= 0.0.3'
|
28
|
+
gem.add_dependency 'ruby-prof', '~> 0.15', '>= 0.15.1'
|
25
29
|
|
26
|
-
gem.add_development_dependency '
|
27
|
-
gem.add_development_dependency '
|
28
|
-
gem.add_development_dependency '
|
29
|
-
gem.add_development_dependency '
|
30
|
+
gem.add_development_dependency 'rake', '~> 10.3', '>= 10.3.2'
|
31
|
+
gem.add_development_dependency 'turn', '~> 0.9', '>= 0.9.7'
|
32
|
+
gem.add_development_dependency 'minitest', '~> 4', '>= 4.7.5'
|
33
|
+
gem.add_development_dependency 'simplecov', '~> 0.8', '>= 0.8.2'
|
34
|
+
gem.add_development_dependency 'shoulda-context', '~> 1.2', '>= 1.2.1'
|
35
|
+
gem.add_development_dependency 'coveralls', '~> 0.7'
|
30
36
|
end
|
metadata
CHANGED
@@ -1,189 +1,363 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: transrate
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.
|
4
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+
version: 0.2.0
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
|
-
- Richard Smith
|
7
|
+
- Richard Smith-Unna
|
8
|
+
- Chris Boursnell
|
8
9
|
autorequire:
|
9
10
|
bindir: bin
|
10
11
|
cert_chain: []
|
11
|
-
date: 2014-
|
12
|
+
date: 2014-07-08 00:00:00.000000000 Z
|
12
13
|
dependencies:
|
13
14
|
- !ruby/object:Gem::Dependency
|
14
|
-
name:
|
15
|
+
name: yell
|
15
16
|
requirement: !ruby/object:Gem::Requirement
|
16
17
|
requirements:
|
17
|
-
- -
|
18
|
+
- - ~>
|
19
|
+
- !ruby/object:Gem::Version
|
20
|
+
version: '2.0'
|
21
|
+
- - '>='
|
18
22
|
- !ruby/object:Gem::Version
|
19
|
-
version:
|
23
|
+
version: 2.0.4
|
20
24
|
type: :runtime
|
21
25
|
prerelease: false
|
22
26
|
version_requirements: !ruby/object:Gem::Requirement
|
23
27
|
requirements:
|
24
|
-
- -
|
28
|
+
- - ~>
|
29
|
+
- !ruby/object:Gem::Version
|
30
|
+
version: '2.0'
|
31
|
+
- - '>='
|
25
32
|
- !ruby/object:Gem::Version
|
26
|
-
version:
|
33
|
+
version: 2.0.4
|
27
34
|
- !ruby/object:Gem::Dependency
|
28
35
|
name: trollop
|
29
36
|
requirement: !ruby/object:Gem::Requirement
|
30
37
|
requirements:
|
31
|
-
- -
|
38
|
+
- - ~>
|
32
39
|
- !ruby/object:Gem::Version
|
33
|
-
version: '0'
|
40
|
+
version: '2.0'
|
34
41
|
type: :runtime
|
35
42
|
prerelease: false
|
36
43
|
version_requirements: !ruby/object:Gem::Requirement
|
37
44
|
requirements:
|
38
|
-
- -
|
45
|
+
- - ~>
|
39
46
|
- !ruby/object:Gem::Version
|
40
|
-
version: '0'
|
47
|
+
version: '2.0'
|
48
|
+
- !ruby/object:Gem::Dependency
|
49
|
+
name: bindeps
|
50
|
+
requirement: !ruby/object:Gem::Requirement
|
51
|
+
requirements:
|
52
|
+
- - ~>
|
53
|
+
- !ruby/object:Gem::Version
|
54
|
+
version: '0.0'
|
55
|
+
- - '>='
|
56
|
+
- !ruby/object:Gem::Version
|
57
|
+
version: 0.0.7
|
58
|
+
type: :runtime
|
59
|
+
prerelease: false
|
60
|
+
version_requirements: !ruby/object:Gem::Requirement
|
61
|
+
requirements:
|
62
|
+
- - ~>
|
63
|
+
- !ruby/object:Gem::Version
|
64
|
+
version: '0.0'
|
65
|
+
- - '>='
|
66
|
+
- !ruby/object:Gem::Version
|
67
|
+
version: 0.0.7
|
41
68
|
- !ruby/object:Gem::Dependency
|
42
69
|
name: which
|
43
70
|
requirement: !ruby/object:Gem::Requirement
|
44
71
|
requirements:
|
45
|
-
- -
|
72
|
+
- - ~>
|
46
73
|
- !ruby/object:Gem::Version
|
47
|
-
version: '0'
|
74
|
+
version: '0.0'
|
75
|
+
- - '>='
|
76
|
+
- !ruby/object:Gem::Version
|
77
|
+
version: 0.0.2
|
48
78
|
type: :runtime
|
49
79
|
prerelease: false
|
50
80
|
version_requirements: !ruby/object:Gem::Requirement
|
51
81
|
requirements:
|
52
|
-
- -
|
82
|
+
- - ~>
|
83
|
+
- !ruby/object:Gem::Version
|
84
|
+
version: '0.0'
|
85
|
+
- - '>='
|
53
86
|
- !ruby/object:Gem::Version
|
54
|
-
version:
|
87
|
+
version: 0.0.2
|
55
88
|
- !ruby/object:Gem::Dependency
|
56
89
|
name: bio
|
57
90
|
requirement: !ruby/object:Gem::Requirement
|
58
91
|
requirements:
|
59
|
-
- -
|
92
|
+
- - ~>
|
60
93
|
- !ruby/object:Gem::Version
|
61
|
-
version: '
|
94
|
+
version: '1.4'
|
95
|
+
- - '>='
|
96
|
+
- !ruby/object:Gem::Version
|
97
|
+
version: 1.4.3
|
62
98
|
type: :runtime
|
63
99
|
prerelease: false
|
64
100
|
version_requirements: !ruby/object:Gem::Requirement
|
65
101
|
requirements:
|
66
|
-
- -
|
102
|
+
- - ~>
|
103
|
+
- !ruby/object:Gem::Version
|
104
|
+
version: '1.4'
|
105
|
+
- - '>='
|
67
106
|
- !ruby/object:Gem::Version
|
68
|
-
version:
|
107
|
+
version: 1.4.3
|
69
108
|
- !ruby/object:Gem::Dependency
|
70
|
-
name:
|
109
|
+
name: bio-samtools
|
71
110
|
requirement: !ruby/object:Gem::Requirement
|
72
111
|
requirements:
|
73
|
-
- -
|
112
|
+
- - ~>
|
74
113
|
- !ruby/object:Gem::Version
|
75
|
-
version: '0'
|
114
|
+
version: '2.0'
|
115
|
+
- - '>='
|
116
|
+
- !ruby/object:Gem::Version
|
117
|
+
version: 2.0.5
|
76
118
|
type: :runtime
|
77
119
|
prerelease: false
|
78
120
|
version_requirements: !ruby/object:Gem::Requirement
|
79
121
|
requirements:
|
80
|
-
- -
|
122
|
+
- - ~>
|
123
|
+
- !ruby/object:Gem::Version
|
124
|
+
version: '2.0'
|
125
|
+
- - '>='
|
81
126
|
- !ruby/object:Gem::Version
|
82
|
-
version:
|
127
|
+
version: 2.0.5
|
83
128
|
- !ruby/object:Gem::Dependency
|
84
129
|
name: RubyInline
|
85
130
|
requirement: !ruby/object:Gem::Requirement
|
86
131
|
requirements:
|
87
|
-
- -
|
132
|
+
- - ~>
|
88
133
|
- !ruby/object:Gem::Version
|
89
134
|
version: '3.12'
|
90
135
|
type: :runtime
|
91
136
|
prerelease: false
|
92
137
|
version_requirements: !ruby/object:Gem::Requirement
|
93
138
|
requirements:
|
94
|
-
- -
|
139
|
+
- - ~>
|
95
140
|
- !ruby/object:Gem::Version
|
96
141
|
version: '3.12'
|
142
|
+
- !ruby/object:Gem::Dependency
|
143
|
+
name: crb-blast
|
144
|
+
requirement: !ruby/object:Gem::Requirement
|
145
|
+
requirements:
|
146
|
+
- - ~>
|
147
|
+
- !ruby/object:Gem::Version
|
148
|
+
version: '0.2'
|
149
|
+
type: :runtime
|
150
|
+
prerelease: false
|
151
|
+
version_requirements: !ruby/object:Gem::Requirement
|
152
|
+
requirements:
|
153
|
+
- - ~>
|
154
|
+
- !ruby/object:Gem::Version
|
155
|
+
version: '0.2'
|
156
|
+
- !ruby/object:Gem::Dependency
|
157
|
+
name: bettersam
|
158
|
+
requirement: !ruby/object:Gem::Requirement
|
159
|
+
requirements:
|
160
|
+
- - ~>
|
161
|
+
- !ruby/object:Gem::Version
|
162
|
+
version: '0.0'
|
163
|
+
- - '>='
|
164
|
+
- !ruby/object:Gem::Version
|
165
|
+
version: 0.0.3
|
166
|
+
type: :runtime
|
167
|
+
prerelease: false
|
168
|
+
version_requirements: !ruby/object:Gem::Requirement
|
169
|
+
requirements:
|
170
|
+
- - ~>
|
171
|
+
- !ruby/object:Gem::Version
|
172
|
+
version: '0.0'
|
173
|
+
- - '>='
|
174
|
+
- !ruby/object:Gem::Version
|
175
|
+
version: 0.0.3
|
176
|
+
- !ruby/object:Gem::Dependency
|
177
|
+
name: ruby-prof
|
178
|
+
requirement: !ruby/object:Gem::Requirement
|
179
|
+
requirements:
|
180
|
+
- - ~>
|
181
|
+
- !ruby/object:Gem::Version
|
182
|
+
version: '0.15'
|
183
|
+
- - '>='
|
184
|
+
- !ruby/object:Gem::Version
|
185
|
+
version: 0.15.1
|
186
|
+
type: :runtime
|
187
|
+
prerelease: false
|
188
|
+
version_requirements: !ruby/object:Gem::Requirement
|
189
|
+
requirements:
|
190
|
+
- - ~>
|
191
|
+
- !ruby/object:Gem::Version
|
192
|
+
version: '0.15'
|
193
|
+
- - '>='
|
194
|
+
- !ruby/object:Gem::Version
|
195
|
+
version: 0.15.1
|
196
|
+
- !ruby/object:Gem::Dependency
|
197
|
+
name: rake
|
198
|
+
requirement: !ruby/object:Gem::Requirement
|
199
|
+
requirements:
|
200
|
+
- - ~>
|
201
|
+
- !ruby/object:Gem::Version
|
202
|
+
version: '10.3'
|
203
|
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- - '>='
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- !ruby/object:Gem::Version
|
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version: 10.3.2
|
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type: :development
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prerelease: false
|
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version_requirements: !ruby/object:Gem::Requirement
|
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requirements:
|
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- - ~>
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- !ruby/object:Gem::Version
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version: '10.3'
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- - '>='
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- !ruby/object:Gem::Version
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version: 10.3.2
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97
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|
- !ruby/object:Gem::Dependency
|
98
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|
name: turn
|
99
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|
requirement: !ruby/object:Gem::Requirement
|
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|
requirements:
|
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- -
|
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- - ~>
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- !ruby/object:Gem::Version
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version: '0.9'
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- - '>='
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- !ruby/object:Gem::Version
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version: 0.9.7
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
|
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requirements:
|
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- - ~>
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- !ruby/object:Gem::Version
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version: '0.9'
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- - '>='
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- !ruby/object:Gem::Version
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version: 0.9.7
|
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- !ruby/object:Gem::Dependency
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name: minitest
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requirement: !ruby/object:Gem::Requirement
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requirements:
|
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- - ~>
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- !ruby/object:Gem::Version
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version: '4'
|
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- - '>='
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102
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- !ruby/object:Gem::Version
|
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|
-
version:
|
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|
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version: 4.7.5
|
104
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type: :development
|
105
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prerelease: false
|
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
|
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- -
|
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|
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- - ~>
|
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- !ruby/object:Gem::Version
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version: '
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version: '4'
|
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- - '>='
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- !ruby/object:Gem::Version
|
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version: 4.7.5
|
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name: simplecov
|
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requirement: !ruby/object:Gem::Requirement
|
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requirements:
|
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- -
|
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- - ~>
|
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- !ruby/object:Gem::Version
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version: '0.8'
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- - '>='
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- !ruby/object:Gem::Version
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|
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version:
|
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|
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version: 0.8.2
|
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type: :development
|
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|
prerelease: false
|
120
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|
version_requirements: !ruby/object:Gem::Requirement
|
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requirements:
|
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- -
|
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|
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- - ~>
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- !ruby/object:Gem::Version
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version: '0.8'
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- - '>='
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- !ruby/object:Gem::Version
|
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version:
|
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version: 0.8.2
|
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|
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|
name: shoulda-context
|
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|
requirement: !ruby/object:Gem::Requirement
|
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requirements:
|
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|
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- -
|
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|
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- - ~>
|
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|
- !ruby/object:Gem::Version
|
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|
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version: '
|
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|
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version: '1.2'
|
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- - '>='
|
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|
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- !ruby/object:Gem::Version
|
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|
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version: 1.2.1
|
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|
type: :development
|
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|
prerelease: false
|
134
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|
version_requirements: !ruby/object:Gem::Requirement
|
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|
requirements:
|
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|
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- -
|
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|
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- - ~>
|
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|
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- !ruby/object:Gem::Version
|
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|
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version: '1.2'
|
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|
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|
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|
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|
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|
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version:
|
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|
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version: 1.2.1
|
139
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|
- !ruby/object:Gem::Dependency
|
140
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|
name: coveralls
|
141
298
|
requirement: !ruby/object:Gem::Requirement
|
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|
requirements:
|
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|
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- -
|
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|
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- - ~>
|
144
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|
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|
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|
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version: 0.
|
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|
+
version: '0.7'
|
146
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|
type: :development
|
147
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|
prerelease: false
|
148
305
|
version_requirements: !ruby/object:Gem::Requirement
|
149
306
|
requirements:
|
150
|
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- -
|
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|
+
- - ~>
|
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308
|
- !ruby/object:Gem::Version
|
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|
-
version: 0.
|
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|
-
description:
|
154
|
-
assemblies
|
309
|
+
version: '0.7'
|
310
|
+
description: ' a library and command-line tool for quality assessment of de-novo transcriptome
|
311
|
+
assemblies '
|
155
312
|
email: rds45@cam.ac.uk
|
156
313
|
executables:
|
157
314
|
- transrate
|
158
315
|
extensions: []
|
159
316
|
extra_rdoc_files: []
|
160
317
|
files:
|
161
|
-
-
|
318
|
+
- .gitignore
|
319
|
+
- .travis.yml
|
162
320
|
- Gemfile
|
163
321
|
- LICENSE
|
164
322
|
- README.md
|
165
323
|
- Rakefile
|
166
324
|
- bin/transrate
|
325
|
+
- deps/deps.yaml
|
167
326
|
- lib/transrate.rb
|
168
327
|
- lib/transrate/assembly.rb
|
169
328
|
- lib/transrate/bowtie2.rb
|
329
|
+
- lib/transrate/cmd.rb
|
170
330
|
- lib/transrate/comparative_metrics.rb
|
331
|
+
- lib/transrate/contig.rb
|
332
|
+
- lib/transrate/contig_metrics.rb
|
171
333
|
- lib/transrate/dimension_reduce.rb
|
172
|
-
- lib/transrate/express.rb
|
173
|
-
- lib/transrate/log.rb
|
174
334
|
- lib/transrate/metric.rb
|
175
|
-
- lib/transrate/rb_hit.rb
|
176
335
|
- lib/transrate/read_metrics.rb
|
177
|
-
- lib/transrate/
|
336
|
+
- lib/transrate/samtools.rb
|
178
337
|
- lib/transrate/transrater.rb
|
179
|
-
- lib/transrate/usearch.rb
|
180
338
|
- lib/transrate/version.rb
|
181
339
|
- lib/transrate/writer.rb
|
182
|
-
- test/
|
340
|
+
- test/data/150uncovered.l.fq
|
341
|
+
- test/data/150uncovered.r.fq
|
342
|
+
- test/data/Os.protein.2.fa
|
343
|
+
- test/data/Os.protein.fa
|
344
|
+
- test/data/assembly.2.fa
|
345
|
+
- test/data/assembly.fasta
|
346
|
+
- test/data/bridging_reads.l.fastq
|
347
|
+
- test/data/bridging_reads.r.fastq
|
348
|
+
- test/data/sorghum_transcript.fa
|
349
|
+
- test/data/tiny.sam
|
183
350
|
- test/helper.rb
|
351
|
+
- test/test_bowtie.rb
|
352
|
+
- test/test_cmd.rb
|
353
|
+
- test/test_comp_metrics.rb
|
354
|
+
- test/test_contig.rb
|
355
|
+
- test/test_contig_metrics.rb
|
184
356
|
- test/test_inline.rb
|
185
|
-
- test/
|
186
|
-
- test/
|
357
|
+
- test/test_read_metrics.rb
|
358
|
+
- test/test_samtools.rb
|
359
|
+
- test/test_transrate.rb
|
360
|
+
- test/test_transrater.rb
|
187
361
|
- transrate.gemspec
|
188
362
|
homepage: https://github.com/Blahah/transrate
|
189
363
|
licenses:
|
@@ -195,18 +369,19 @@ require_paths:
|
|
195
369
|
- lib
|
196
370
|
required_ruby_version: !ruby/object:Gem::Requirement
|
197
371
|
requirements:
|
198
|
-
- -
|
372
|
+
- - '>='
|
199
373
|
- !ruby/object:Gem::Version
|
200
374
|
version: '0'
|
201
375
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
202
376
|
requirements:
|
203
|
-
- -
|
377
|
+
- - '>='
|
204
378
|
- !ruby/object:Gem::Version
|
205
379
|
version: '0'
|
206
380
|
requirements: []
|
207
381
|
rubyforge_project:
|
208
|
-
rubygems_version: 2.
|
382
|
+
rubygems_version: 2.0.6
|
209
383
|
signing_key:
|
210
384
|
specification_version: 4
|
211
385
|
summary: quality assessment of de-novo transcriptome assemblies
|
212
386
|
test_files: []
|
387
|
+
has_rdoc:
|