vienna_rna 0.9.1 → 0.9.2

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 (4) hide show
  1. checksums.yaml +4 -4
  2. data/lib/vienna_rna/global/rna.rb +7 -1
  3. data/lib/vienna_rna/graphing/r.rb +19 -11
  4. metadata +15 -15
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
1
1
  ---
2
2
  SHA1:
3
- metadata.gz: a899fb4d340d38517ca0ea8a6cf40972c633f943
4
- data.tar.gz: 61102bfc0d277cdb89da81c7114f2f4a1a370eff
3
+ metadata.gz: 75269157e25be08827f08546fffdb90af43be397
4
+ data.tar.gz: a8b2094c492af287894e3219e3328233ecf31340
5
5
  SHA512:
6
- metadata.gz: d105473a36561ba4d1cc9b49f4d95af0ce2d571682d1239af88ea2c7a5b37b004c00cabc3fb96eb6a9b8f9ab97b99a89d91564fa352661774d6e8d84615777c0
7
- data.tar.gz: 7afc4799420d2ad31c116e3d9f9c6a65f91bbea83ca86f840e1c3d10d98cae9c0dad5ba2facd6050cc3629d14a53cf88b0f484a653ab86257a557887716f7b27
6
+ metadata.gz: 26a7068d00b8181041fc0ea12d38a25b65724ff3eb0dd2e910821bbea27c4bfa7317835956242881cac3e1cc64442e6cfc3a23e3135d5e16f2382c0648dbaa7a
7
+ data.tar.gz: bd6799d8ca85f2ddf712fac00e97eb17700b01218e2a99579a0aba94ee2d0fd7a899bff56a473b8b719f7eec8112ab110dd02372a43f5326b19d107aac4ea829
data/lib/vienna_rna/global/rna.rb CHANGED
@@ -46,7 +46,7 @@ module ViennaRna
46
46
  end
47
47
 
48
48
  def initialize(sequence: "", structure: "", second_structure: "", raw_data: {})
49
- @sequence, @raw_data = sequence, raw_data
49
+ @sequence, @raw_data = sequence.kind_of?(Rna) ? sequence.seq : sequence, raw_data
50
50
 
51
51
  [:structure, :second_structure].each do |structure_symbol|
52
52
  instance_variable_set(
@@ -55,6 +55,12 @@ module ViennaRna
55
55
  when :empty then empty_structure
56
56
  when :mfe then RNA(sequence).run(:fold).mfe_rna.structure
57
57
  when String then structure_value
58
+ when Hash then
59
+ if structure_value.keys.count > 1
60
+ ViennaRna.debugger { "The following options hash has more than one key. This will probably produce unpredictable results: %s" % structure_value.inspect }
61
+ end
62
+
63
+ RNA(sequence).run(*structure_value.keys, *structure_value.values).mfe_rna.structure
58
64
  end
59
65
  )
60
66
  end
data/lib/vienna_rna/graphing/r.rb CHANGED
@@ -26,7 +26,7 @@ module ViennaRna
26
26
 
27
27
  r.assign("legend.titles", data.each_with_index.map { |hash, index| hash[:legend] || "Line #{index + 1}" })
28
28
  r.eval("line.colors <- rainbow(%d)" % data.size)
29
- r.eval("plot(0, 0, type = 'n', cex = .75, xlab = '', ylab = '', xlim = c(%d, %d), ylim = c(%d, %d))" % [
29
+ r.eval("plot(0, 0, type = 'n', cex = .75, cex.axis = .9, xlab = '', ylab = '', xlim = c(%d, %d), ylim = c(%d, %d))" % [
30
30
  x_range.min, x_range.max, y_range.min, y_range.max
31
31
  ])
32
32
 
@@ -47,9 +47,11 @@ module ViennaRna
47
47
 
48
48
  r.eval <<-STR
49
49
  title(
50
- xlab = "#{x_label}",
51
- ylab = "#{y_label}",
52
- main = "#{title || 'Line Graph'}"
50
+ xlab = "#{x_label}",
51
+ ylab = "#{y_label}",
52
+ main = "#{title || 'Line Graph'}",
53
+ cex.main = .9,
54
+ cex.lab = .9
53
55
  )
54
56
  STR
55
57
 
@@ -61,7 +63,8 @@ module ViennaRna
61
63
  bty = "n",
62
64
  col = line.colors,
63
65
  lty = rep(1, #{data.size}),
64
- pch = 0:#{data.size}
66
+ pch = 0:#{data.size},
67
+ cex = .9
65
68
  )
66
69
  STR
67
70
  end
@@ -74,10 +77,10 @@ module ViennaRna
74
77
  overlay([{ data: data }], title: title, type: type, x_label: x_label, y_label: y_label, legend: false, filename: filename)
75
78
  end
76
79
 
77
- def histogram(data, title: nil, x_label: "Bins", bin_size: 1, relative: false, filename: false)
80
+ def histogram(data, title: nil, x_label: "Bins", num_bins: false, bin_size: 1, x_arrow: false, relative: false, filename: false)
78
81
  half = bin_size / 2.0
79
82
  range = Range.new((data.min - half).floor, (data.max + half).ceil)
80
- breaks = (range.min + half).step(range.max + half, bin_size).to_a
83
+ breaks = num_bins ? num_bins : (range.min + half).step(range.max + half, bin_size).to_a
81
84
 
82
85
  graph do |r|
83
86
  r.assign("histogram.data", data)
@@ -91,13 +94,18 @@ module ViennaRna
91
94
  r.eval <<-STR
92
95
  hist(
93
96
  histogram.data,
94
- breaks = histogram.breaks,
95
- xlab = "#{x_label} (width: #{bin_size})",
96
- main = "#{title || 'Histogram'}",
97
- freq = #{relative ? 'FALSE' : 'TRUE'}
97
+ breaks = histogram.breaks,
98
+ xlab = "#{x_label}",
99
+ main = "#{title || 'Histogram'}",
100
+ freq = #{relative ? 'F' : 'T'},
101
+ cex.main = 0.9,
102
+ cex.lab = 0.9,
103
+ cex.axis = 0.9
98
104
  )
99
105
  STR
100
106
 
107
+ r.eval("abline(v = #{x_arrow}, lty = 'dashed')") if x_arrow
108
+
101
109
  r.eval("dev.off()") if writing_file?(filename)
102
110
  end
103
111
  end
metadata CHANGED
@@ -1,83 +1,83 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: vienna_rna
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.9.1
4
+ version: 0.9.2
5
5
  platform: ruby
6
6
  authors:
7
7
  - Evan Senter
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2013-09-19 00:00:00.000000000 Z
11
+ date: 2013-10-07 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: bio
15
15
  requirement: !ruby/object:Gem::Requirement
16
16
  requirements:
17
- - - '>='
17
+ - - ">="
18
18
  - !ruby/object:Gem::Version
19
19
  version: 1.4.2
20
20
  type: :runtime
21
21
  prerelease: false
22
22
  version_requirements: !ruby/object:Gem::Requirement
23
23
  requirements:
24
- - - '>='
24
+ - - ">="
25
25
  - !ruby/object:Gem::Version
26
26
  version: 1.4.2
27
27
  - !ruby/object:Gem::Dependency
28
28
  name: activesupport
29
29
  requirement: !ruby/object:Gem::Requirement
30
30
  requirements:
31
- - - '>='
31
+ - - ">="
32
32
  - !ruby/object:Gem::Version
33
33
  version: '3.2'
34
34
  type: :runtime
35
35
  prerelease: false
36
36
  version_requirements: !ruby/object:Gem::Requirement
37
37
  requirements:
38
- - - '>='
38
+ - - ">="
39
39
  - !ruby/object:Gem::Version
40
40
  version: '3.2'
41
41
  - !ruby/object:Gem::Dependency
42
42
  name: shuffle
43
43
  requirement: !ruby/object:Gem::Requirement
44
44
  requirements:
45
- - - '>='
45
+ - - ">="
46
46
  - !ruby/object:Gem::Version
47
47
  version: 0.1.0
48
48
  type: :runtime
49
49
  prerelease: false
50
50
  version_requirements: !ruby/object:Gem::Requirement
51
51
  requirements:
52
- - - '>='
52
+ - - ">="
53
53
  - !ruby/object:Gem::Version
54
54
  version: 0.1.0
55
55
  - !ruby/object:Gem::Dependency
56
56
  name: rinruby
57
57
  requirement: !ruby/object:Gem::Requirement
58
58
  requirements:
59
- - - '>='
59
+ - - ">="
60
60
  - !ruby/object:Gem::Version
61
61
  version: 2.0.3
62
62
  type: :runtime
63
63
  prerelease: false
64
64
  version_requirements: !ruby/object:Gem::Requirement
65
65
  requirements:
66
- - - '>='
66
+ - - ">="
67
67
  - !ruby/object:Gem::Version
68
68
  version: 2.0.3
69
69
  - !ruby/object:Gem::Dependency
70
70
  name: rroc
71
71
  requirement: !ruby/object:Gem::Requirement
72
72
  requirements:
73
- - - '>='
73
+ - - ">="
74
74
  - !ruby/object:Gem::Version
75
75
  version: 0.1.1
76
76
  type: :runtime
77
77
  prerelease: false
78
78
  version_requirements: !ruby/object:Gem::Requirement
79
79
  requirements:
80
- - - '>='
80
+ - - ">="
81
81
  - !ruby/object:Gem::Version
82
82
  version: 0.1.1
83
83
  description: A Ruby 2.0 API for interacting with command line tools involving RNA
@@ -113,17 +113,17 @@ require_paths:
113
113
  - lib
114
114
  required_ruby_version: !ruby/object:Gem::Requirement
115
115
  requirements:
116
- - - '>='
116
+ - - ">="
117
117
  - !ruby/object:Gem::Version
118
118
  version: '0'
119
119
  required_rubygems_version: !ruby/object:Gem::Requirement
120
120
  requirements:
121
- - - '>='
121
+ - - ">="
122
122
  - !ruby/object:Gem::Version
123
123
  version: '0'
124
124
  requirements: []
125
125
  rubyforge_project:
126
- rubygems_version: 2.1.2
126
+ rubygems_version: 2.1.4
127
127
  signing_key:
128
128
  specification_version: 4
129
129
  summary: Bindings to the Vienna RNA package, and other major command line utilities