Class: Feature

Inherits:
Object
  • Object
show all
Defined in:
lib/gene_assembler/gff_feature.rb

Direct Known Subclasses

Master_feature

Constant Summary collapse

@@undefined_features = 
0

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(source, type, start, stop, score, strand, phase, attribs) ⇒ Feature

Returns a new instance of Feature.



4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
 
# File 'lib/gene_assembler/gff_feature.rb', line 4

def initialize(source, type, start, stop, score, strand, phase, attribs)
	@source=source
	@type=type
	@start=start.to_i
	@stop=stop.to_i
	if score=='.'
		@score='.'
	else
		@score=score.to_f
	end
	@strand=strand
	if phase=='.'
		@phase='.'
	else
		@phase=phase.to_i
	end
	@attribs=attribs
	if attrib('Name').nil? #Añade el atributo name en base a la ID de forma automatica
		@attribs['Name']=attrib('ID')
   else
     revised_name = @attribs['Name']
     revised_name.gsub!(';','-')
     @attribs['Name'] = revised_name
	end
	@child={}
end

Instance Attribute Details

#attribs ⇒ Object

Returns the value of attribute attribs.



2
3
4
 
# File 'lib/gene_assembler/gff_feature.rb', line 2

def attribs
  @attribs
end

#child ⇒ Object

Returns the value of attribute child.



2
3
4
 
# File 'lib/gene_assembler/gff_feature.rb', line 2

def child
  @child
end

#phase ⇒ Object

Returns the value of attribute phase.



2
3
4
 
# File 'lib/gene_assembler/gff_feature.rb', line 2

def phase
  @phase
end

#score ⇒ Object

Returns the value of attribute score.



2
3
4
 
# File 'lib/gene_assembler/gff_feature.rb', line 2

def score
  @score
end

#source ⇒ Object

Returns the value of attribute source.



2
3
4
 
# File 'lib/gene_assembler/gff_feature.rb', line 2

def source
  @source
end

#start ⇒ Object

Returns the value of attribute start.



2
3
4
 
# File 'lib/gene_assembler/gff_feature.rb', line 2

def start
  @start
end

#stop ⇒ Object

Returns the value of attribute stop.



2
3
4
 
# File 'lib/gene_assembler/gff_feature.rb', line 2

def stop
  @stop
end

#strand ⇒ Object

Returns the value of attribute strand.



2
3
4
 
# File 'lib/gene_assembler/gff_feature.rb', line 2

def strand
  @strand
end

#type ⇒ Object

Returns the value of attribute type.



2
3
4
 
# File 'lib/gene_assembler/gff_feature.rb', line 2

def type
  @type
end

Instance Method Details

#add_attribs(array_attribs) ⇒ Object 



167
168
169
170
171
172
173
 
# File 'lib/gene_assembler/gff_feature.rb', line 167

def add_attribs(array_attribs)
  array_attribs.each do |attrib|
    if !attrib[1].nil?
      @attribs[attrib[0]]=attrib[1]
    end
  end
end

#add_child(source, type, start, stop, score, strand, phase, attribs) ⇒ Object 



31
32
33
34
35
36
37
38
39
40
 
# File 'lib/gene_assembler/gff_feature.rb', line 31

def add_child(source, type, start, stop, score, strand, phase, attribs)
  child=Feature.new(source, type, start, stop, score, strand, phase, attribs)
  if !attribs['ID'].nil?
   		@child[attribs['ID']]=child
   else
   		@child[child.attrib('Parent')+'_'+@@undefined_features.to_s]=child
   		@@undefined_features+=1
   end
   return child
end

#attrib(tag) ⇒ Object 



52
53
54
55
 
# File 'lib/gene_assembler/gff_feature.rb', line 52

def attrib(tag)
	attrib=@attribs[tag]
	return attrib
end

#cds ⇒ Object 



75
76
77
78
79
80
81
82
83
 
# File 'lib/gene_assembler/gff_feature.rb', line 75

def cds
	cds_exones=[]
	@child.each do |key_cds|
		if key_cds[1].type=='CDS'
			cds_exones << [key_cds[1].start, key_cds[1].stop]
		end
	end
	return cds_exones
end

#change_to_type_id_recursive(parent = FALSE) ⇒ Object 



137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
 
# File 'lib/gene_assembler/gff_feature.rb', line 137

def change_to_type_id_recursive(parent=FALSE)
  new_parent="#{attrib('ID')}_#{@type}"
  if !attrib('ID').nil?
    @attribs['ID']=new_parent
  end

  if !attrib('Name').nil?
    @attribs['Name']=new_parent
  end

  if !attrib('Parent').nil? && parent
    @attribs['Parent']=parent
  end
  
  each_child {|child|
    child.change_to_type_id_recursive(new_parent)
  } 
end

#compare(feature) ⇒ Object

Resultado oscila entre 0 y 1



117
118
119
120
121
122
123
124
125
126
127
128
129
 
# File 'lib/gene_assembler/gff_feature.rb', line 117

def compare(feature) #Resultado oscila entre 0 y 1
  overlap=0
  if feature.start >= self.start && feature.start <= self.stop && feature.stop >= self.start && feature.stop <= self.stop
    overlap=feature.length*1.00/self.length
  elsif  self.start >= feature.start && self.start <= feature.stop && self.stop >= feature.start && self.stop <= feature.stop
    overlap=1
  elsif feature.start > self.start && feature.start < self.stop   
    overlap=(self.stop-feature.start)*1.00/self.length
  elsif feature.stop > self.start && feature.stop < self.stop
    overlap=(feature.stop-self.start)*1.00/self.length
  end
  return overlap
end

#count ⇒ Object 



71
72
73
 
# File 'lib/gene_assembler/gff_feature.rb', line 71

def count
	return @child.count
end

#each_child ⇒ Object 



46
47
48
49
50
 
# File 'lib/gene_assembler/gff_feature.rb', line 46

def each_child
  @child.each_value do |child|
    yield child
  end
end

#each_tag_attrib ⇒ Object 



57
58
59
60
61
 
# File 'lib/gene_assembler/gff_feature.rb', line 57

def each_tag_attrib
  @attribs.each do |tag,attrib|
    yield tag,attrib
  end
end

#inspects ⇒ Object 



63
64
65
66
67
68
69
 
# File 'lib/gene_assembler/gff_feature.rb', line 63

def inspects
	print attrib('ID')+" ---> "
	@child.keys.each do |ch|
		print "#{ch} (#{@child[ch].count})\t"
	end
	print "\n"
end

#is_source?(source) ⇒ Boolean

Returns:

  • (Boolean) 


105
106
107
108
109
110
111
112
113
114
115
 
# File 'lib/gene_assembler/gff_feature.rb', line 105

def is_source?(source)
  s=FALSE
  source=[source].flatten
  source.each do |sour|
    if sour == @source
      s=TRUE
      break
    end
  end
  return s
end

#is_type?(type) ⇒ Boolean

Returns:

  • (Boolean) 


93
94
95
96
97
98
99
100
101
102
103
 
# File 'lib/gene_assembler/gff_feature.rb', line 93

def is_type?(type)
  t=FALSE
   type=[type].flatten
   type.each do |typ|
     if typ == @type
       t=TRUE
       break
     end
   end
   return t
end

#length ⇒ Object 



131
132
133
134
 
# File 'lib/gene_assembler/gff_feature.rb', line 131

def length
  length=self.stop-(self.start-1)
  return length
end

#transfer_child(id, child) ⇒ Object 



42
43
44
 
# File 'lib/gene_assembler/gff_feature.rb', line 42

def transfer_child(id,child)
  @child[id]=child
end

#tree(level = 0) ⇒ Object 



85
86
87
88
89
90
91
 
# File 'lib/gene_assembler/gff_feature.rb', line 85

def tree(level=0)
   puts "\t"*level+"#{attrib('ID')}\t\t#{@type}\t#{@source}"
   level+=1
   each_child {|child|
     child.tree(level)
   }
end

#write(file, id) ⇒ Object 



156
157
158
159
160
161
162
163
164
165
 
# File 'lib/gene_assembler/gff_feature.rb', line 156

def write(file,id)
  file.print "#{id}\t#{@source}\t#{@type}\t#{@start}\t#{@stop}\t#{@score}\t#{@strand}\t#{@phase}\t"
  each_tag_attrib {|tag,attrib|
    file.print "#{tag}=#{attrib};"
  }
  file.puts #Print \n
  each_child {|child|
    child.write(file,id)
  }
end