Class: Bio::PolyploidTools::Marker

Inherits:
Object
  • Object
show all
Includes:
Comparable
Defined in:
lib/bio/PolyploidTools/Marker.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(line) ⇒ Marker

Returns a new instance of Marker.



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# File 'lib/bio/PolyploidTools/Marker.rb', line 42

def initialize(line)
  line.chomp!
  @template_sequence = nil
  #INDEX_90K,SNP_ID,SNP_NAME,CHR,COORDINATES_CHR,MAP_ORDER,CHR_ARM,DISTANCE_CM,SEQUENCE
  @index_90k, @snp_id, @snp_name, @chr, @coordinates_chr, @map_order, @chr_arm, @distance_cm, @sequence, @contig = line.split(',')
  parse_sequence_snp
end

Instance Attribute Details

#best_hit ⇒ Object

Returns the value of attribute best_hit.



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# File 'lib/bio/PolyploidTools/Marker.rb', line 6

def best_hit
  @best_hit
end

#chr ⇒ Object

Returns the value of attribute chr.



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# File 'lib/bio/PolyploidTools/Marker.rb', line 10

def chr
  @chr
end

#chr_arm ⇒ Object

Returns the value of attribute chr_arm.



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# File 'lib/bio/PolyploidTools/Marker.rb', line 13

def chr_arm
  @chr_arm
end

#contig ⇒ Object 



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# File 'lib/bio/PolyploidTools/Marker.rb', line 26

def contig
  @contig = best_hit.target_id.chomp if best_hit
  @contig
end

#coordinates_chr ⇒ Object

Returns the value of attribute coordinates_chr.



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# File 'lib/bio/PolyploidTools/Marker.rb', line 11

def coordinates_chr
  @coordinates_chr
end

#distance_cm ⇒ Object

Returns the value of attribute distance_cm.



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# File 'lib/bio/PolyploidTools/Marker.rb', line 14

def distance_cm
  @distance_cm
end

#index_90k ⇒ Object

Returns the value of attribute index_90k.



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# File 'lib/bio/PolyploidTools/Marker.rb', line 7

def index_90k
  @index_90k
end

#map_order ⇒ Object

Returns the value of attribute map_order.



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# File 'lib/bio/PolyploidTools/Marker.rb', line 12

def map_order
  @map_order
end

#original ⇒ Object (readonly)

include Virgola



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# File 'lib/bio/PolyploidTools/Marker.rb', line 5

def original
  @original
end

#sequence ⇒ Object

Returns the value of attribute sequence.



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# File 'lib/bio/PolyploidTools/Marker.rb', line 15

def sequence
  @sequence
end

#snp ⇒ Object (readonly)

include Virgola



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# File 'lib/bio/PolyploidTools/Marker.rb', line 5

def snp
  @snp
end

#snp_id ⇒ Object

Returns the value of attribute snp_id.



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# File 'lib/bio/PolyploidTools/Marker.rb', line 8

def snp_id
  @snp_id
end

#snp_name ⇒ Object

Returns the value of attribute snp_name.



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# File 'lib/bio/PolyploidTools/Marker.rb', line 9

def snp_name
  @snp_name
end

#template_sequence ⇒ Object (readonly)

include Virgola



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# File 'lib/bio/PolyploidTools/Marker.rb', line 5

def template_sequence
  @template_sequence
end

Class Method Details

.parse(filename) ⇒ Object 



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# File 'lib/bio/PolyploidTools/Marker.rb', line 50

def self.parse(filename)
  f = File.open(filename, "r").read
  f.each_line do |line|
    m = Marker.new(line)
    yield m if m.template_sequence

  end
end

Instance Method Details

#<=>(anOter) ⇒ Object 



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# File 'lib/bio/PolyploidTools/Marker.rb', line 35

def <=>(anOter)
 return 0 if anOter.snp_name == @snp_name 
 return @chr_arm <=> anOter.chr_arm  if anOter.chr_arm != @chr_arm
 return @snp_name  <=> anOter.snp_name if anOter.coordinates_chr == @coordinates_chr
 return @coordinates_chr <=> anOter.coordinates_chr    
end

#to_csv ⇒ Object 



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# File 'lib/bio/PolyploidTools/Marker.rb', line 31

def to_csv
  "#{index_90k},#{snp_id},#{snp_name},#{chr},#{coordinates_chr},#{map_order},#{chr_arm},#{distance_cm},#{sequence},#{contig}"
end

#to_fasta ⇒ Object

after_map :parse_sequence_snp



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# File 'lib/bio/PolyploidTools/Marker.rb', line 22

def to_fasta
  ">#{self.snp_name}\n#{self.template_sequence}"
end