transrate 0.3.1 → 1.0.0.alpha.1

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@@ -155,36 +155,12 @@ class TestCompMetrics < Test::Unit::TestCase
155
155
  @reference["LOC_Os01g11360.1"].seq = "A"*200
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  @reference["LOC_Os01g44140.1"].seq = "A"*200
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+ assert_equal true, crb.target_is_prot, "target is prot"
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+ assert_equal false, crb.query_is_prot, "query is prot"
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  # total_length of references should be 4400
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  cov = @comp.coverage crb
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- assert_equal 3600/4400.0, cov, "reference coverage"
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- end
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-
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- should "calculate potential chimera count" do
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- crb = @comp.reciprocal_best_blast
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- # # T1 |---------|
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- # # T2 |---------|
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- # # Q1 |----------------------------| # chimera = true
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-
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- crb.remove_hit("scaf_Os10g39590.1")
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- crb.add_hit("scaf_Os10g39590.1", "LOC_Os03g60760.1",
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- 1, 150, 51, 100, 400, 60) # 0.25
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- crb.add_hit("scaf_Os10g39590.1", "LOC_Os10g39590.1",
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- 200, 350, 51, 100, 400, 60) # 0.25
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-
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- # # T3 |---------|
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- # # T3 |---------|
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- # # Q2 |----------------------------|
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- # # chimera = true because the reference has the region 1-100 duplicated
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- crb.remove_hit("scaf_Os12g21920.1")
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- crb.add_hit("scaf_Os12g21920.1", "LOC_Os12g21920.1",
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- 1, 150, 55, 105, 400, 60) # 0.25
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- crb.add_hit("scaf_Os12g21920.1", "LOC_Os12g21920.1",
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- 200, 350, 51, 100, 400, 60) # 0.25
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-
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- @comp.chimeras crb
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- assert_equal 2/11.0, @comp.p_chimeras
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+ assert_equal 3600/13200.0, cov, "reference coverage"
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  end
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  should "calculate overlap amount" do
@@ -83,6 +83,14 @@ class TestContig < Test::Unit::TestCase
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  assert_equal 7, contig.orf_length, "orf length"
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  end
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85
 
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+ should "get orf length from ATG to stop" do
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+ s = "AAATAGATAGATAGAATGAATCAACTAACTAAATAA"
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+ # seq = Bio::FastaFormat.new ">test\n#{s}\n>test_r\n#{s.reverse}\n"
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+ seq = Bio::FastaFormat.new ">test\n#{s}\n>test_r"
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+ contig = Transrate::Contig.new seq
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+ assert_equal 6, contig.orf_length, "orf length"
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+ end
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+
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  should "not fail on bases that aren't ACGTN" do
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  seq = Bio::FastaFormat.new ">test\nATGCGTGTARATACGCGTAG"
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  contig = Transrate::Contig.new seq
@@ -18,7 +18,7 @@ class TestInline < Test::Unit::TestCase
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  orfs << contig.orf_length
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  end
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  assert_equal 4, orfs.length
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- assert_equal [333, 370, 131, 84], orfs
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+ assert_equal [319, 321, 95, 71], orfs
22
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  end
23
23
 
24
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  should 'find longest orf in sequence' do
@@ -8,8 +8,8 @@ class TestReadMetrics < Test::Unit::TestCase
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  setup do
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9
  query = File.join(File.dirname(__FILE__), 'data',
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  'sorghum_transcript.fa')
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- assembly = Transrate::Assembly.new(query)
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- @read_metrics = Transrate::ReadMetrics.new(assembly)
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+ @assembly = Transrate::Assembly.new(query)
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+ @read_metrics = Transrate::ReadMetrics.new(@assembly)
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  end
14
14
 
15
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  teardown do
@@ -30,30 +30,87 @@ class TestReadMetrics < Test::Unit::TestCase
30
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  Dir.chdir tmpdir do
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  @read_metrics.run(left, right)
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  stats = @read_metrics.read_stats
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- assert @read_metrics.has_run
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- assert_equal 223, stats[:num_pairs], 'number of read pairs'
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- assert_equal 202, stats[:total_mappings], 'number mapping'
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- assert_equal 90.58, stats[:percent_mapping].round(2),
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- 'percent mapping'
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- assert_equal 202, stats[:good_mappings], 'good mapping'
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- assert_equal 90.58,
40
- stats[:pc_good_mapping].round(2),
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+ assert @read_metrics.has_run, "has run"
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+ assert_equal 223, stats[:fragments], 'number of read pairs'
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+ assert_equal 217, stats[:fragments_mapped], 'number mapping'
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+ assert_equal 0.9731, stats[:p_fragments_mapped].round(4),
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+ 'proportion mapping'
38
+ assert_equal 129, stats[:good_mappings], 'good mapping'
39
+ assert_equal 0.5785, stats[:p_good_mapping].round(4),
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  'percent good mapping'
42
- assert_equal 0, stats[:bad_mappings], 'bad mapping'
43
- assert_equal 22.91, stats[:mean_coverage].round(2), 'mean coverage'
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- assert_equal 11, stats[:n_uncovered_bases], 'n uncovered bases'
45
- assert_equal 0.007,
46
- stats[:p_uncovered_bases].round(3),
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- 'p uncovered bases'
41
+ assert_equal 88, stats[:bad_mappings], 'bad mapping'
42
+ assert_equal 2, stats[:potential_bridges], 'bridges'
43
+ assert_equal 2, stats[:contigs_uncovbase], 'uncovered base contig'
44
+ assert_equal 0, stats[:contigs_uncovered], 'uncovered contig'
45
+ assert_equal 0, stats[:contigs_lowcovered], 'lowcovered contig'
46
+ assert_equal 2, stats[:contigs_good], 'good contigs'
47
+ end
48
+ end
49
+ end
50
+
51
+ should "get metrics for individual contigs" do
52
+ left = File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
53
+ right = File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
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+ Dir.mktmpdir do |tmpdir|
55
+ Dir.chdir tmpdir do
56
+ @read_metrics.run(left, right)
57
+ contigs = []
58
+ @assembly.each do |name, contig|
59
+ contigs << contig
60
+ end
61
+ a = contigs[0].read_metrics
62
+ b = contigs[1].read_metrics
63
+
64
+ edit_a = a[:p_seq_true].round(5)
65
+ edit_b = b[:p_seq_true].round(5)
66
+ assert_equal 0.98342, edit_a, "edit distance 1"
67
+ assert_equal 0.96645, edit_b, "edit distance 2"
68
+
69
+ assert_equal 0.59524, a[:p_good].round(5), "proportion of good mappings"
70
+ assert_equal 0.59398, b[:p_good].round(5), "proportion of good mappings"
71
+
72
+ # uncovered bases
73
+ unc_a = contigs[0].uncovered_bases
74
+ unc_b = contigs[1].uncovered_bases
75
+ assert_equal 11, unc_a, "uncovered bases"
76
+ assert_equal 1, unc_b, "uncovered bases"
77
+
78
+ prop_unc_a = a[:p_bases_covered]
79
+ prop_unc_b = b[:p_bases_covered]
80
+ assert_equal 0.98497, prop_unc_a.round(5), "proportion covered bases"
81
+ assert_equal 0.99878, prop_unc_b.round(5), "proportion covered bases"
82
+
83
+ end
84
+ end
85
+ end
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+
87
+ should "get segmentation probability for individual contigs" do
88
+ left = File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
89
+ right = File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
90
+ Dir.mktmpdir do |tmpdir|
91
+ Dir.chdir tmpdir do
92
+ @read_metrics.run(left, right)
93
+ contigs = []
94
+ @assembly.each do |name, contig|
95
+ contigs << contig
96
+ end
97
+ a = contigs[0].read_metrics
98
+ b = contigs[1].read_metrics
99
+
100
+ edit_a = a[:p_not_segmented].round(5)
101
+ edit_b = b[:p_not_segmented].round(5)
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+ assert_equal 0.11444, edit_a, "probability not segmented 1"
103
+ assert_equal 0.79629, edit_b, "probability not segmented 2"
104
+
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105
  end
49
106
  end
50
107
  end
51
108
 
52
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  should "find read pairs that support scaffolding" do
53
- left = File.join(File.dirname(__FILE__), 'data', 'bridging_reads.l.fastq')
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+ left = File.join(File.dirname(__FILE__),
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+ 'data', 'bridging_reads.l.fastq')
54
112
  right = File.join(File.dirname(__FILE__),
55
- 'data',
56
- 'bridging_reads.r.fastq')
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+ 'data', 'bridging_reads.r.fastq')
57
114
  Dir.mktmpdir do |tmpdir|
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115
  Dir.chdir tmpdir do
59
116
  @read_metrics.run(left, right)
@@ -63,6 +120,38 @@ class TestReadMetrics < Test::Unit::TestCase
63
120
  end
64
121
  end
65
122
 
123
+ should "run on a list of input fastq files" do
124
+ left = []
125
+ right = []
126
+ left << File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
127
+ right << File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
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+ left << File.join(File.dirname(__FILE__),
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+ 'data', 'bridging_reads.l.fastq')
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+ right << File.join(File.dirname(__FILE__),
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+ 'data', 'bridging_reads.r.fastq')
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+ Dir.mktmpdir do |tmpdir|
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+ Dir.chdir tmpdir do
134
+ @read_metrics.run(left.join(","), right.join(","))
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+ stats = @read_metrics.read_stats
136
+ assert_equal 233, stats[:fragments], 'number of read pairs'
137
+ end
138
+ end
139
+
140
+ end
141
+
142
+ should "calculate read length by scanning fastq files" do
143
+ left = []
144
+ right = []
145
+ left << File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
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+ right << File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
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+ left << File.join(File.dirname(__FILE__),
148
+ 'data', 'bridging_reads.l.fastq')
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+ right << File.join(File.dirname(__FILE__),
150
+ 'data', 'bridging_reads.r.fastq')
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+ @read_metrics.get_read_length(left.join(","), right.join(","))
152
+ assert_equal 100, @read_metrics.read_length
153
+ end
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+
66
155
  end
67
156
 
68
157
  end
@@ -8,7 +8,7 @@ class TestTransrater < Test::Unit::TestCase
8
8
  context "transrater" do
9
9
 
10
10
  setup do
11
- @assembly = File.join(File.dirname(__FILE__), 'data', 'assembly.2.fa')
11
+ @assembly = File.join(File.dirname(__FILE__), 'data', 'sorghum_transcript.fa')
12
12
  @reference = File.join(File.dirname(__FILE__), 'data', 'Os.protein.2.fa')
13
13
  @rater = Transrate::Transrater.new(@assembly, @reference)
14
14
  @left = File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
@@ -39,8 +39,8 @@ class TestTransrater < Test::Unit::TestCase
39
39
  Dir.mktmpdir do |tmpdir|
40
40
  Dir.chdir tmpdir do
41
41
  stats = @rater.assembly_metrics
42
- assert_equal 1566, stats.n50
43
- assert_equal 10331, stats.n_bases
42
+ assert_equal 823, stats.n50
43
+ assert_equal 1555, stats.n_bases
44
44
  end
45
45
  end
46
46
  end
@@ -49,7 +49,7 @@ class TestTransrater < Test::Unit::TestCase
49
49
  Dir.mktmpdir do |tmpdir|
50
50
  Dir.chdir tmpdir do
51
51
  stats = @rater.read_metrics(@left, @right)
52
- assert_equal 223, stats.read_stats[:num_pairs]
52
+ assert_equal 223, stats.read_stats[:fragments]
53
53
  end
54
54
  end
55
55
  end
@@ -59,7 +59,7 @@ class TestTransrater < Test::Unit::TestCase
59
59
  Dir.chdir tmpdir do
60
60
  all = @rater.all_metrics(@left, @right)
61
61
  score = @rater.assembly_score
62
- assert_equal 0.55815, score.round(5) # regression test
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+ assert_equal 0.40755, score.round(5) # regression test
63
63
  end
64
64
  end
65
65
  end
@@ -19,12 +19,9 @@ Gem::Specification.new do |gem|
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19
 
20
20
  gem.add_dependency 'yell', '~> 2.0', '>= 2.0.4'
21
21
  gem.add_dependency 'trollop', '~> 2.0'
22
- gem.add_dependency 'bindeps', '~> 0.0', '>= 0.0.8'
23
- gem.add_dependency 'which', '~> 0.0', '>= 0.0.2'
22
+ gem.add_dependency 'bindeps', '~> 0.1', '>= 0.1.0'
24
23
  gem.add_dependency 'bio', '~> 1.4', '>= 1.4.3'
25
- gem.add_dependency 'bio-samtools', '~> 2.0', '>= 2.0.5'
26
- gem.add_dependency 'crb-blast', '~> 0.4', '>= 0.4.0'
27
- gem.add_dependency 'bettersam', '~> 0.0', '>= 0.0.3'
24
+ gem.add_dependency 'crb-blast', '~> 0.4', '>= 0.4.2'
28
25
  gem.add_dependency 'ruby-prof', '~> 0.15', '>= 0.15.1'
29
26
 
30
27
  gem.add_development_dependency 'rake', '~> 10.3', '>= 10.3.2'
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: transrate
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.3.1
4
+ version: 1.0.0.alpha.1
5
5
  platform: ruby
6
6
  authors:
7
7
  - Richard Smith-Unna
@@ -9,318 +9,258 @@ authors:
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2014-07-25 00:00:00.000000000 Z
12
+ date: 2014-10-15 00:00:00.000000000 Z
13
13
  dependencies:
14
14
  - !ruby/object:Gem::Dependency
15
15
  name: yell
16
16
  requirement: !ruby/object:Gem::Requirement
17
17
  requirements:
18
- - - ~>
18
+ - - "~>"
19
19
  - !ruby/object:Gem::Version
20
20
  version: '2.0'
21
- - - '>='
21
+ - - ">="
22
22
  - !ruby/object:Gem::Version
23
23
  version: 2.0.4
24
24
  type: :runtime
25
25
  prerelease: false
26
26
  version_requirements: !ruby/object:Gem::Requirement
27
27
  requirements:
28
- - - ~>
28
+ - - "~>"
29
29
  - !ruby/object:Gem::Version
30
30
  version: '2.0'
31
- - - '>='
31
+ - - ">="
32
32
  - !ruby/object:Gem::Version
33
33
  version: 2.0.4
34
34
  - !ruby/object:Gem::Dependency
35
35
  name: trollop
36
36
  requirement: !ruby/object:Gem::Requirement
37
37
  requirements:
38
- - - ~>
38
+ - - "~>"
39
39
  - !ruby/object:Gem::Version
40
40
  version: '2.0'
41
41
  type: :runtime
42
42
  prerelease: false
43
43
  version_requirements: !ruby/object:Gem::Requirement
44
44
  requirements:
45
- - - ~>
45
+ - - "~>"
46
46
  - !ruby/object:Gem::Version
47
47
  version: '2.0'
48
48
  - !ruby/object:Gem::Dependency
49
49
  name: bindeps
50
50
  requirement: !ruby/object:Gem::Requirement
51
51
  requirements:
52
- - - ~>
52
+ - - "~>"
53
53
  - !ruby/object:Gem::Version
54
- version: '0.0'
55
- - - '>='
54
+ version: '0.1'
55
+ - - ">="
56
56
  - !ruby/object:Gem::Version
57
- version: 0.0.8
57
+ version: 0.1.0
58
58
  type: :runtime
59
59
  prerelease: false
60
60
  version_requirements: !ruby/object:Gem::Requirement
61
61
  requirements:
62
- - - ~>
62
+ - - "~>"
63
63
  - !ruby/object:Gem::Version
64
- version: '0.0'
65
- - - '>='
64
+ version: '0.1'
65
+ - - ">="
66
66
  - !ruby/object:Gem::Version
67
- version: 0.0.8
68
- - !ruby/object:Gem::Dependency
69
- name: which
70
- requirement: !ruby/object:Gem::Requirement
71
- requirements:
72
- - - ~>
73
- - !ruby/object:Gem::Version
74
- version: '0.0'
75
- - - '>='
76
- - !ruby/object:Gem::Version
77
- version: 0.0.2
78
- type: :runtime
79
- prerelease: false
80
- version_requirements: !ruby/object:Gem::Requirement
81
- requirements:
82
- - - ~>
83
- - !ruby/object:Gem::Version
84
- version: '0.0'
85
- - - '>='
86
- - !ruby/object:Gem::Version
87
- version: 0.0.2
67
+ version: 0.1.0
88
68
  - !ruby/object:Gem::Dependency
89
69
  name: bio
90
70
  requirement: !ruby/object:Gem::Requirement
91
71
  requirements:
92
- - - ~>
72
+ - - "~>"
93
73
  - !ruby/object:Gem::Version
94
74
  version: '1.4'
95
- - - '>='
75
+ - - ">="
96
76
  - !ruby/object:Gem::Version
97
77
  version: 1.4.3
98
78
  type: :runtime
99
79
  prerelease: false
100
80
  version_requirements: !ruby/object:Gem::Requirement
101
81
  requirements:
102
- - - ~>
82
+ - - "~>"
103
83
  - !ruby/object:Gem::Version
104
84
  version: '1.4'
105
- - - '>='
85
+ - - ">="
106
86
  - !ruby/object:Gem::Version
107
87
  version: 1.4.3
108
- - !ruby/object:Gem::Dependency
109
- name: bio-samtools
110
- requirement: !ruby/object:Gem::Requirement
111
- requirements:
112
- - - ~>
113
- - !ruby/object:Gem::Version
114
- version: '2.0'
115
- - - '>='
116
- - !ruby/object:Gem::Version
117
- version: 2.0.5
118
- type: :runtime
119
- prerelease: false
120
- version_requirements: !ruby/object:Gem::Requirement
121
- requirements:
122
- - - ~>
123
- - !ruby/object:Gem::Version
124
- version: '2.0'
125
- - - '>='
126
- - !ruby/object:Gem::Version
127
- version: 2.0.5
128
88
  - !ruby/object:Gem::Dependency
129
89
  name: crb-blast
130
90
  requirement: !ruby/object:Gem::Requirement
131
91
  requirements:
132
- - - ~>
92
+ - - "~>"
133
93
  - !ruby/object:Gem::Version
134
94
  version: '0.4'
135
- - - '>='
95
+ - - ">="
136
96
  - !ruby/object:Gem::Version
137
- version: 0.4.0
97
+ version: 0.4.2
138
98
  type: :runtime
139
99
  prerelease: false
140
100
  version_requirements: !ruby/object:Gem::Requirement
141
101
  requirements:
142
- - - ~>
102
+ - - "~>"
143
103
  - !ruby/object:Gem::Version
144
104
  version: '0.4'
145
- - - '>='
146
- - !ruby/object:Gem::Version
147
- version: 0.4.0
148
- - !ruby/object:Gem::Dependency
149
- name: bettersam
150
- requirement: !ruby/object:Gem::Requirement
151
- requirements:
152
- - - ~>
153
- - !ruby/object:Gem::Version
154
- version: '0.0'
155
- - - '>='
105
+ - - ">="
156
106
  - !ruby/object:Gem::Version
157
- version: 0.0.3
158
- type: :runtime
159
- prerelease: false
160
- version_requirements: !ruby/object:Gem::Requirement
161
- requirements:
162
- - - ~>
163
- - !ruby/object:Gem::Version
164
- version: '0.0'
165
- - - '>='
166
- - !ruby/object:Gem::Version
167
- version: 0.0.3
107
+ version: 0.4.2
168
108
  - !ruby/object:Gem::Dependency
169
109
  name: ruby-prof
170
110
  requirement: !ruby/object:Gem::Requirement
171
111
  requirements:
172
- - - ~>
112
+ - - "~>"
173
113
  - !ruby/object:Gem::Version
174
114
  version: '0.15'
175
- - - '>='
115
+ - - ">="
176
116
  - !ruby/object:Gem::Version
177
117
  version: 0.15.1
178
118
  type: :runtime
179
119
  prerelease: false
180
120
  version_requirements: !ruby/object:Gem::Requirement
181
121
  requirements:
182
- - - ~>
122
+ - - "~>"
183
123
  - !ruby/object:Gem::Version
184
124
  version: '0.15'
185
- - - '>='
125
+ - - ">="
186
126
  - !ruby/object:Gem::Version
187
127
  version: 0.15.1
188
128
  - !ruby/object:Gem::Dependency
189
129
  name: rake
190
130
  requirement: !ruby/object:Gem::Requirement
191
131
  requirements:
192
- - - ~>
132
+ - - "~>"
193
133
  - !ruby/object:Gem::Version
194
134
  version: '10.3'
195
- - - '>='
135
+ - - ">="
196
136
  - !ruby/object:Gem::Version
197
137
  version: 10.3.2
198
138
  type: :development
199
139
  prerelease: false
200
140
  version_requirements: !ruby/object:Gem::Requirement
201
141
  requirements:
202
- - - ~>
142
+ - - "~>"
203
143
  - !ruby/object:Gem::Version
204
144
  version: '10.3'
205
- - - '>='
145
+ - - ">="
206
146
  - !ruby/object:Gem::Version
207
147
  version: 10.3.2
208
148
  - !ruby/object:Gem::Dependency
209
149
  name: rake-compiler
210
150
  requirement: !ruby/object:Gem::Requirement
211
151
  requirements:
212
- - - ~>
152
+ - - "~>"
213
153
  - !ruby/object:Gem::Version
214
154
  version: '0.9'
215
- - - '>='
155
+ - - ">="
216
156
  - !ruby/object:Gem::Version
217
157
  version: 0.9.2
218
158
  type: :development
219
159
  prerelease: false
220
160
  version_requirements: !ruby/object:Gem::Requirement
221
161
  requirements:
222
- - - ~>
162
+ - - "~>"
223
163
  - !ruby/object:Gem::Version
224
164
  version: '0.9'
225
- - - '>='
165
+ - - ">="
226
166
  - !ruby/object:Gem::Version
227
167
  version: 0.9.2
228
168
  - !ruby/object:Gem::Dependency
229
169
  name: turn
230
170
  requirement: !ruby/object:Gem::Requirement
231
171
  requirements:
232
- - - ~>
172
+ - - "~>"
233
173
  - !ruby/object:Gem::Version
234
174
  version: '0.9'
235
- - - '>='
175
+ - - ">="
236
176
  - !ruby/object:Gem::Version
237
177
  version: 0.9.7
238
178
  type: :development
239
179
  prerelease: false
240
180
  version_requirements: !ruby/object:Gem::Requirement
241
181
  requirements:
242
- - - ~>
182
+ - - "~>"
243
183
  - !ruby/object:Gem::Version
244
184
  version: '0.9'
245
- - - '>='
185
+ - - ">="
246
186
  - !ruby/object:Gem::Version
247
187
  version: 0.9.7
248
188
  - !ruby/object:Gem::Dependency
249
189
  name: minitest
250
190
  requirement: !ruby/object:Gem::Requirement
251
191
  requirements:
252
- - - ~>
192
+ - - "~>"
253
193
  - !ruby/object:Gem::Version
254
194
  version: '4'
255
- - - '>='
195
+ - - ">="
256
196
  - !ruby/object:Gem::Version
257
197
  version: 4.7.5
258
198
  type: :development
259
199
  prerelease: false
260
200
  version_requirements: !ruby/object:Gem::Requirement
261
201
  requirements:
262
- - - ~>
202
+ - - "~>"
263
203
  - !ruby/object:Gem::Version
264
204
  version: '4'
265
- - - '>='
205
+ - - ">="
266
206
  - !ruby/object:Gem::Version
267
207
  version: 4.7.5
268
208
  - !ruby/object:Gem::Dependency
269
209
  name: simplecov
270
210
  requirement: !ruby/object:Gem::Requirement
271
211
  requirements:
272
- - - ~>
212
+ - - "~>"
273
213
  - !ruby/object:Gem::Version
274
214
  version: '0.8'
275
- - - '>='
215
+ - - ">="
276
216
  - !ruby/object:Gem::Version
277
217
  version: 0.8.2
278
218
  type: :development
279
219
  prerelease: false
280
220
  version_requirements: !ruby/object:Gem::Requirement
281
221
  requirements:
282
- - - ~>
222
+ - - "~>"
283
223
  - !ruby/object:Gem::Version
284
224
  version: '0.8'
285
- - - '>='
225
+ - - ">="
286
226
  - !ruby/object:Gem::Version
287
227
  version: 0.8.2
288
228
  - !ruby/object:Gem::Dependency
289
229
  name: shoulda-context
290
230
  requirement: !ruby/object:Gem::Requirement
291
231
  requirements:
292
- - - ~>
232
+ - - "~>"
293
233
  - !ruby/object:Gem::Version
294
234
  version: '1.2'
295
- - - '>='
235
+ - - ">="
296
236
  - !ruby/object:Gem::Version
297
237
  version: 1.2.1
298
238
  type: :development
299
239
  prerelease: false
300
240
  version_requirements: !ruby/object:Gem::Requirement
301
241
  requirements:
302
- - - ~>
242
+ - - "~>"
303
243
  - !ruby/object:Gem::Version
304
244
  version: '1.2'
305
- - - '>='
245
+ - - ">="
306
246
  - !ruby/object:Gem::Version
307
247
  version: 1.2.1
308
248
  - !ruby/object:Gem::Dependency
309
249
  name: coveralls
310
250
  requirement: !ruby/object:Gem::Requirement
311
251
  requirements:
312
- - - ~>
252
+ - - "~>"
313
253
  - !ruby/object:Gem::Version
314
254
  version: '0.7'
315
255
  type: :development
316
256
  prerelease: false
317
257
  version_requirements: !ruby/object:Gem::Requirement
318
258
  requirements:
319
- - - ~>
259
+ - - "~>"
320
260
  - !ruby/object:Gem::Version
321
261
  version: '0.7'
322
- description: ' a library and command-line tool for quality assessment of de-novo transcriptome
323
- assemblies '
262
+ description: " a library and command-line tool for quality assessment of de-novo transcriptome
263
+ assemblies "
324
264
  email: rds45@cam.ac.uk
325
265
  executables:
326
266
  - transrate
@@ -328,8 +268,8 @@ extensions:
328
268
  - ext/transrate/extconf.rb
329
269
  extra_rdoc_files: []
330
270
  files:
331
- - .gitignore
332
- - .travis.yml
271
+ - ".gitignore"
272
+ - ".travis.yml"
333
273
  - Gemfile
334
274
  - LICENSE
335
275
  - README.md
@@ -341,15 +281,14 @@ files:
341
281
  - ext/transrate/transrate.c
342
282
  - lib/transrate.rb
343
283
  - lib/transrate/assembly.rb
344
- - lib/transrate/bowtie2.rb
345
284
  - lib/transrate/cmd.rb
346
285
  - lib/transrate/comparative_metrics.rb
347
286
  - lib/transrate/contig.rb
348
287
  - lib/transrate/contig_metrics.rb
349
- - lib/transrate/dimension_reduce.rb
350
- - lib/transrate/metric.rb
288
+ - lib/transrate/express.rb
351
289
  - lib/transrate/read_metrics.rb
352
290
  - lib/transrate/samtools.rb
291
+ - lib/transrate/snap.rb
353
292
  - lib/transrate/transrater.rb
354
293
  - lib/transrate/version.rb
355
294
  - lib/transrate/writer.rb
@@ -365,7 +304,6 @@ files:
365
304
  - test/data/tiny.sam
366
305
  - test/helper.rb
367
306
  - test/test_bin.rb
368
- - test/test_bowtie.rb
369
307
  - test/test_cmd.rb
370
308
  - test/test_comp_metrics.rb
371
309
  - test/test_contig.rb
@@ -387,19 +325,18 @@ require_paths:
387
325
  - ext
388
326
  required_ruby_version: !ruby/object:Gem::Requirement
389
327
  requirements:
390
- - - '>='
328
+ - - ">="
391
329
  - !ruby/object:Gem::Version
392
330
  version: '0'
393
331
  required_rubygems_version: !ruby/object:Gem::Requirement
394
332
  requirements:
395
- - - '>='
333
+ - - ">"
396
334
  - !ruby/object:Gem::Version
397
- version: '0'
335
+ version: 1.3.1
398
336
  requirements: []
399
337
  rubyforge_project:
400
- rubygems_version: 2.1.4
338
+ rubygems_version: 2.2.2
401
339
  signing_key:
402
340
  specification_version: 4
403
341
  summary: quality assessment of de-novo transcriptome assemblies
404
342
  test_files: []
405
- has_rdoc: