wrnap 0.4.0 → 0.5.1

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Files changed (5) hide show
  1. checksums.yaml +4 -4
  2. data/lib/wrnap/global/rna.rb +3 -3
  3. data/lib/wrnap/global/rna/context.rb +101 -89
  4. data/lib/wrnap/version.rb +1 -1
  5. metadata +1 -1
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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- metadata.gz: 28e711a4fd54857a15fa5ce3beac1f3b3d5e99824883d44b20ec5a73deff48e6191ef38f64c4d85a8198e481736c0a467ca1b88bea2f1fb243610913d47e79e7
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data/lib/wrnap/global/rna.rb CHANGED
@@ -44,8 +44,8 @@ module Wrnap
44
44
  end
45
45
  end
46
46
 
47
- def init_from_context(context: [], rna: [])
48
- init_from_string(Context.init_from_entrez(*context), *rna)
47
+ def init_from_context(*context, coords: {}, rna: {})
48
+ Context.init_from_entrez(*context, coords: coords, rna: rna)
49
49
  end
50
50
 
51
51
  def init_from_self(rna)
@@ -62,7 +62,7 @@ module Wrnap
62
62
  end
63
63
 
64
64
  def initialize(sequence: "", structure: "", second_structure: "", comment: "")
65
- @sequence, @comment = sequence.kind_of?(Rna) ? sequence.seq : sequence, comment
65
+ @sequence, @comment = (sequence.kind_of?(Rna) ? sequence.seq : sequence).upcase, comment
66
66
 
67
67
  [:structure, :second_structure].each do |structure_symbol|
68
68
  instance_variable_set(
data/lib/wrnap/global/rna/context.rb CHANGED
@@ -1,120 +1,132 @@
1
1
  module Wrnap
2
2
  module Global
3
- class Context < Rna
4
- attr_reader :accession, :from, :to, :coord_options
5
-
6
- class << self
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- def init_from_entrez(accession, from, to, coord_options = {})
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- new(
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- accession: accession,
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- from: from,
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- to: to,
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- coord_options: coord_options
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- )
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- end
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+ class Rna
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+ class Context < Rna
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+ attr_reader :accession, :from, :to, :coord_options
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+
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+ class << self
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+ def init_from_entrez(accession, from, to, options = {})
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+ new(
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+ accession: accession,
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+ from: from,
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+ to: to,
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+ options: options
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+ )
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+ end
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16
 
16
- def init_from_string(sequence, accession, from, to, coord_options = {})
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- new(
18
- sequence: sequence,
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- accession: accession,
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- from: from,
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- to: to,
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- coord_options: coord_options
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- )
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+ def init_from_string(sequence, accession, from, to, options = {})
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+ new(
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+ sequence: sequence,
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+ accession: accession,
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+ from: from,
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+ to: to,
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+ options: options
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+ )
25
+ end
24
26
  end
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- end
26
27
 
27
- def initialize(sequence: nil, accession: nil, from: nil, to: nil, coord_options: {})
28
- @accession, @from, @to, @coord_options = accession, from, to, coord_options
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+ def initialize(sequence: nil, accession: nil, from: nil, to: nil, options: {})
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+ options = { coords: {}, rna: {} }.merge(options)
29
30
 
30
- validate_coord_options
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+ @accession, @from, @to, @coord_options = accession, from, to, options[:coords]
31
32
 
32
- if sequence
33
- @raw_sequence = (sequence.is_a?(String) ? Bio::Sequence::NA.new(sequence) : sequence).upcase
34
- end
35
- end
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+ validate_coord_options
36
34
 
37
- def validate_coord_options
38
- unless coord_options.empty?
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- unless coord_options.keys == Set.new(%i|direction length|)
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- raise ArgumentError.new("coord_options keys must contain only :direction, :length, found: %s" % coord_options.keys)
35
+ if sequence
36
+ @raw_sequence = (sequence.is_a?(String) ? Bio::Sequence::NA.new(sequence) : sequence).upcase
41
37
  end
42
38
 
43
- unless (length = coord_options[:length]).is_a?(Integer) && length > 0
44
- raise ArgumentError.new("coord_options length must be greater than 0, found: %d" % length)
45
- end
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+ super({
40
+ sequence: self.sequence,
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+ structure: options[:rna][:structure] || options[:rna][:str_1] || options[:rna][:str],
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+ second_structure: options[:rna][:second_structure] || options[:rna][:str_2],
43
+ comment: options[:rna][:comment] || options[:rna][:name]
44
+ })
46
45
 
47
- unless [:up, :down, :both, 5, 3].include?(direction = coord_options[:direction])
48
- raise ArgumentError.new("coord_options directions is not a valid key, found: %s" % direction)
49
- end
46
+ remove_instance_variable(:@sequence)
50
47
  end
51
- end
52
48
 
53
- def up_coord
54
- [from, to].min
55
- end
49
+ def validate_coord_options
50
+ unless coord_options.empty?
51
+ unless Set.new(coord_options.keys) == Set.new(%i|direction length|)
52
+ raise ArgumentError.new("coord_options keys must contain only [:direction, :length], found: %s" % coord_options.keys)
53
+ end
56
54
 
57
- def down_coord
58
- [from, to].max
59
- end
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+ unless (length = coord_options[:length]).is_a?(Integer) && length > 0
56
+ raise ArgumentError.new("coord_options length must be greater than 0, found: %d" % length)
57
+ end
60
58
 
61
- def seq_from
62
- up_coord + coord_window.min
63
- end
59
+ unless [:up, :down, :both, 5, 3].include?(direction = coord_options[:direction])
60
+ raise ArgumentError.new("coord_options directions is not a valid key, found: %s" % direction)
61
+ end
62
+ end
63
+ end
64
64
 
65
- def seq_to
66
- up_coord + coord_window.max
67
- end
65
+ def up_coord
66
+ [from, to].min
67
+ end
68
68
 
69
- def strand
70
- plus_strand? ? :plus : :minus
71
- end
69
+ def down_coord
70
+ [from, to].max
71
+ end
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72
 
73
- def plus_strand?
74
- to > from
75
- end
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+ def seq_from
74
+ up_coord + coord_window.min
75
+ end
76
76
 
77
- def minus_strand?
78
- !plus_strand?
79
- end
77
+ def seq_to
78
+ up_coord + coord_window.max
79
+ end
80
80
 
81
- def sequence
82
- @raw_sequence ||= Entrez.rna_sequence_from_entrez(accession, up_coord, coord_window)
83
- @raw_sequence = minus_strand? ? @raw_sequence.complement : @raw_sequence
84
- end
81
+ def strand
82
+ plus_strand? ? :plus : :minus
83
+ end
85
84
 
86
- alias :seq :sequence
85
+ def plus_strand?
86
+ to > from
87
+ end
87
88
 
88
- def extend!(coord_options = {})
89
- tap do
90
- @coord_options = coord_options unless coord_options.empty?
91
- validate_coord_options
92
- @extended = true
93
- remove_instance_variable(:@raw_sequence)
89
+ def minus_strand?
90
+ !plus_strand?
94
91
  end
95
- end
96
92
 
97
- def extended?
98
- @extended
99
- end
93
+ def sequence
94
+ if @raw_sequence
95
+ @raw_sequence
96
+ else
97
+ entrez_sequence = Entrez.rna_sequence_from_entrez(accession, up_coord, coord_window)
98
+ @raw_sequence = (minus_strand? ? entrez_sequence.complement : entrez_sequence).upcase
99
+ end
100
+ end
100
101
 
101
- def coord_window
102
- # This does not support extending the range in both directions, though it should be easy to do.
103
- # Options from coord_options ex: { length: 300, direction: 3 }, { length: 250, direction: :both }, { length: 200, direction: :down }
104
- range = 0..(down_coord - up_coord)
102
+ alias :seq :sequence
105
103
 
106
- if coord_options[:length] && coord_options[:direction]
107
- if coord_options[:direction] == :both
108
- Range.new(range.min - coord_options[:length], range.max + coord_options[:length])
109
- else
110
- case [coord_options[:direction], strand]
111
- when [3, :plus], [:down, :plus], [5, :minus], [:up, :minus] then Range.new(range.min, range.max + coord_options[:length])
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- when [5, :plus], [:up, :plus], [3, :minus], [:down, :minus] then Range.new(range.min - coord_options[:length], range.max)
113
- else Wrnap.debugger { "WARNING: value for :direction key in sequence retreival needs to be one of 5, 3, :both - found (%s)" % coord_options[:direction].inspect }
104
+ def extend!(coord_options = {})
105
+ self.class.init_from_entrez(accession, from, to, coords: coord_options)
106
+ end
107
+
108
+ def coord_window
109
+ # This does not support extending the range in both directions, though it should be easy to do.
110
+ # Options from coord_options ex: { length: 300, direction: 3 }, { length: 250, direction: :both }, { length: 200, direction: :down }
111
+ range = 0..(down_coord - up_coord)
112
+
113
+ if coord_options[:length] && coord_options[:direction]
114
+ if coord_options[:direction] == :both
115
+ Range.new(range.min - coord_options[:length], range.max + coord_options[:length])
116
+ else
117
+ case [coord_options[:direction], strand]
118
+ when [3, :plus], [:down, :plus], [5, :minus], [:up, :minus] then Range.new(range.min, range.max + coord_options[:length])
119
+ when [5, :plus], [:up, :plus], [3, :minus], [:down, :minus] then Range.new(range.min - coord_options[:length], range.max)
120
+ else Wrnap.debugger { "WARNING: value for :direction key in sequence retreival needs to be one of 5, 3, :both - found (%s)" % coord_options[:direction].inspect }
121
+ end
114
122
  end
123
+ else
124
+ range
115
125
  end
116
- else
117
- range
126
+ end
127
+
128
+ def inspect
129
+ super.gsub(/((\w(::)?)+)>$/) { |_| "%s %d %s %d %s>" % [accession, from, plus_strand? ? ?+ : ?-, to, $1] }
118
130
  end
119
131
  end
120
132
  end
data/lib/wrnap/version.rb CHANGED
@@ -1,3 +1,3 @@
1
1
  module Wrnap
2
- VERSION = "0.4.0"
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+ VERSION = "0.5.1"
3
3
  end
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: wrnap
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  version: !ruby/object:Gem::Version
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- version: 0.4.0
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+ version: 0.5.1
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  platform: ruby
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  authors:
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7
  - Evan Senter