Class: Bio::Util::MrnaModel

Inherits:
GFF::GFF3::Record
  • Object
show all
Defined in:
lib/bio/utils/bio-synreport.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(gff_line) ⇒ MrnaModel

Returns a new instance of MrnaModel.



10
11
12
13
 
# File 'lib/bio/utils/bio-synreport.rb', line 10

def initialize(gff_line)
  super gff_line
  @cds = []
end

Instance Attribute Details

#cds ⇒ Object

Returns the value of attribute cds.



9
10
11
 
# File 'lib/bio/utils/bio-synreport.rb', line 9

def cds
  @cds
end

#seq ⇒ Object

Returns the value of attribute seq.



9
10
11
 
# File 'lib/bio/utils/bio-synreport.rb', line 9

def seq
  @seq
end

Instance Method Details

#cds_end ⇒ Object 



24
25
26
 
# File 'lib/bio/utils/bio-synreport.rb', line 24

def cds_end
  @cds.flatten.max
end

#cds_start ⇒ Object 



20
21
22
 
# File 'lib/bio/utils/bio-synreport.rb', line 20

def cds_start
  @cds.flatten.min
end

#codon_and_index(point) ⇒ Object

returns codon and position of nucleotide



60
61
62
63
64
65
66
67
 
# File 'lib/bio/utils/bio-synreport.rb', line 60

def codon_and_index(point)
   distance_into_cds = get_nt_number_in_cds point
   codon_idx = codon_index distance_into_cds
   codon_list = codon_array
   codon = codon_list[codon_idx]
   pos = codon_position(distance_into_cds)
   [codon,pos]
end

#codon_array ⇒ Object 



51
52
53
54
 
# File 'lib/bio/utils/bio-synreport.rb', line 51

def codon_array
  codon_array = []; Bio::Sequence::NA.new(self.seq).window_search(3,3) {|b| codon_array << b}
  codon_array
end

#codon_index(dist) ⇒ Object 



43
44
45
 
# File 'lib/bio/utils/bio-synreport.rb', line 43

def codon_index(dist)
  (dist - 1) / 3
end

#codon_position(dist) ⇒ Object 



47
48
49
 
# File 'lib/bio/utils/bio-synreport.rb', line 47

def codon_position(dist)
  (dist - 1) % 3
end

#get_nt_number_in_cds(point) ⇒ Object 



28
29
30
31
32
33
34
35
36
37
38
39
40
41
 
# File 'lib/bio/utils/bio-synreport.rb', line 28

def get_nt_number_in_cds(point)
  to_count = @cds.sort.select {|a| a.first <= point}
  in_block = to_count.pop
  distance_in = to_count.inject(1) {|tot, b| tot + ( b.last - b.first) + 1 }
  overhang =  point - in_block.first 
  left_section = distance_in + overhang
  
  if self.strand == '-'
      length = @cds.sort.inject(0) {|tot, b| tot + ( b.last - b.first) + 1 }
      return length - left_section + 1
  end
  
  return left_section
end

#includes?(seq, point) ⇒ Boolean

Returns:

  • (Boolean) 


15
16
17
18
 
# File 'lib/bio/utils/bio-synreport.rb', line 15

def includes?(seq, point)
  return true if self.seqname == seq and point.to_i >= self.cds_start and point.to_i <= self.cds_end
  false
end

#nt ⇒ Object 



56
57
 
# File 'lib/bio/utils/bio-synreport.rb', line 56

def nt
end

#substitution_info(point, alt) ⇒ Object 



69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
 
# File 'lib/bio/utils/bio-synreport.rb', line 69

def substitution_info(point,alt)
      codon, position = codon_and_index(point)
      new_codon = codon.dup
      new_codon[position] = alt.downcase
      
      a = Bio::Sequence::NA.new(codon).translate.codes.first
      b =  Bio::Sequence::NA.new(new_codon).translate.codes.first
      sub_type = a == b ? "SYN" : "NON_SYN"
      return {#:id => self.gffid, 
              :chr => self.seqname, 
              :strand => self.strand, 
              :position => point,
              :original_codon => codon, 
              :original_residue => a || 'stop', 
              :mutant_codon => new_codon, 
              :mutant_residue =>b || 'stop', 
              :position_in_codon => position + 1, 
              :substitution_type => sub_type
              }

end