Class: Bio::NCBI::Dbsnp::Bitfield

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/ncbi/dbsnp/bitfield.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(byte_stream) ⇒ Bitfield

Returns a new instance of Bitfield.



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# File 'lib/bio/ncbi/dbsnp/bitfield.rb', line 6

def initialize(byte_stream)
  @byte_stream = byte_stream
  ver = version
  raise "Unsupported bitfield version (ver.#{ver})" unless ver == 5
end

Instance Attribute Details

#byte_stream ⇒ Object (readonly)

Returns the value of attribute byte_stream.



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# File 'lib/bio/ncbi/dbsnp/bitfield.rb', line 12

def byte_stream
  @byte_stream
end

Class Method Details

.parse(bitfield_str) ⇒ Object 



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# File 'lib/bio/ncbi/dbsnp/bitfield.rb', line 14

def self.parse(bitfield_str)
  byte_stream = Array.new
  bitfield_str.tr("_","").chars.each_slice(2) do |byte_str|
    byte_stream << Integer("0x#{byte_str.join("")}")
  end
  self.new(byte_stream)
end

Instance Method Details

#allele_frequency ⇒ Object

field F4



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# File 'lib/bio/ncbi/dbsnp/bitfield.rb', line 98

def allele_frequency
  fld = field(4)
  res = Array.new
  res << :mutation                         if bit? fld, 0b1000
  res << :validated                        if bit? fld, 0b0100
  res << :maf_gt5_each_and_all_populations if bit? fld, 0b0010
  res << :maf_gt5_in_1plus_populations     if bit? fld, 0b0001
  res
end

#field(fnum) ⇒ Object 



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# File 'lib/bio/ncbi/dbsnp/bitfield.rb', line 22

def field(fnum)
  case fnum
  when 0
    byte_stream[0]
  when 1
    (byte_stream[2] << 8) + byte_stream[1]
  when 2
    (byte_stream[4] << 8) + byte_stream[3]
else
    byte_stream[fnum + 2]
  end
end

#gene_function ⇒ Object

field F2



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# File 'lib/bio/ncbi/dbsnp/bitfield.rb', line 63

def gene_function
  fld = field(2)
  res = Array.new
  res << :stop_loss                 if bit? fld, 0b10_0000_0000_0000
  res << :non_synonymous_frameshift if bit? fld, 0b01_0000_0000_0000
  res << :non_synonymous_missense   if bit? fld, 0b00_1000_0000_0000
  res << :stop_gain                 if bit? fld, 0b00_0100_0000_0000
  res << :reference                 if bit? fld, 0b00_0010_0000_0000
  res << :synonymous                if bit? fld, 0b00_0001_0000_0000
  res << :utr_3p                    if bit? fld, 0b00_0000_1000_0000
  res << :utr_5p                    if bit? fld, 0b00_0000_0100_0000
  res << :acceptor_splice_site      if bit? fld, 0b00_0000_0010_0000
  res << :donor_splice_site         if bit? fld, 0b00_0000_0001_0000
  res << :intron                    if bit? fld, 0b00_0000_0000_1000
  res << :gene_region_3p            if bit? fld, 0b00_0000_0000_0100
  res << :gene_region_5p            if bit? fld, 0b00_0000_0000_0010
  res << :gene_segment              if bit? fld, 0b00_0000_0000_0001
  res
end

#genotype ⇒ Object

field F5



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# File 'lib/bio/ncbi/dbsnp/bitfield.rb', line 109

def genotype
  fld = field(5)
  res = Array.new
  res << :high_density          if bit? fld, 0b0100
  res << :haplotype_tagging_set if bit? fld, 0b0010
  res << :available             if bit? fld, 0b0001
  res
end

#mapping ⇒ Object

field F3



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# File 'lib/bio/ncbi/dbsnp/bitfield.rb', line 84

def mapping
  fld = field(3)
  res = Array.new
  res << :other_snp         if bit? fld, 0b1_0000
  res << :assembly_conflict if bit? fld, 0b0_1000
  res << :assembly_specific if bit? fld, 0b0_0100
  res << :weight3           if bit? fld, 0b0_0011
  res << :weight2           if bit? fld, 0b0_0010
  res << :weight1           if bit? fld, 0b0_0001
  res << :unmapped if (fld & 0b0000_0011) == 0
  res
end

#phenotype ⇒ Object

field F7



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# File 'lib/bio/ncbi/dbsnp/bitfield.rb', line 133

def phenotype
  fld = field(7)
  res = Array.new
  res << :mesh_disease            if bit? fld, 0b1000_0000
  res << :clinical_diagnosis      if bit? fld, 0b0100_0000
  res << :transciption_factor     if bit? fld, 0b0010_0000
  res << :locus_specific_database if bit? fld, 0b0001_0000
  res << :dbgap_p_valued          if bit? fld, 0b0000_1000
  res << :dbgap_lod               if bit? fld, 0b0000_0100
  res << :tpa_gwas_page           if bit? fld, 0b0000_0010
  res << :omim_omia               if bit? fld, 0b0000_0001
  res
end

#quality_check ⇒ Object

field F9



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# File 'lib/bio/ncbi/dbsnp/bitfield.rb', line 172

def quality_check
  fld = field(9)
  res = Array.new
  res << :suspect                           if bit? fld, 0b00_0000_0100_0000
  res << :somatic                           if bit? fld, 0b00_0000_0010_0000
  res << :reference_allele_missing          if bit? fld, 0b00_0000_0001_0000
  res << :withdrawn_by_submitter            if bit? fld, 0b00_0000_0000_1000
  res << :no_allele_overlap                 if bit? fld, 0b00_0000_0000_0100
  res << :strain_specific_fiexed_defference if bit? fld, 0b00_0000_0000_0010
  res << :genotype_conflict                 if bit? fld, 0b00_0000_0000_0001
  res
end

#resource_link ⇒ Object

field F1



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# File 'lib/bio/ncbi/dbsnp/bitfield.rb', line 41

def resource_link
  fld = field(1)
  res = Array.new
  res << :clinical               if bit? fld, 0b100_0000_0000_0000
  res << :precious               if bit? fld, 0b010_0000_0000_0000
  res << :provisional_tpa        if bit? fld, 0b001_0000_0000_0000
  res << :pubmed_central_article if bit? fld, 0b000_1000_0000_0000
  res << :short_read_archive     if bit? fld, 0b000_0100_0000_0000
  res << :organism_dblink        if bit? fld, 0b000_0010_0000_0000
  res << :mgc_clone              if bit? fld, 0b000_0001_0000_0000
  res << :trace_archive          if bit? fld, 0b000_0000_1000_0000
  res << :assemby_archive        if bit? fld, 0b000_0000_0100_0000
  res << :entrez_geo             if bit? fld, 0b000_0000_0010_0000
  res << :peobe_db               if bit? fld, 0b000_0000_0001_0000
  res << :entrez_gene            if bit? fld, 0b000_0000_0000_1000
  res << :entrez_sts             if bit? fld, 0b000_0000_0000_0100
  res << :threed_structure       if bit? fld, 0b000_0000_0000_0010
  res << :submitter_link_out     if bit? fld, 0b000_0000_0000_0001
  res
end

#validation ⇒ Object

field F6



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# File 'lib/bio/ncbi/dbsnp/bitfield.rb', line 119

def validation
  fld = field(6)
  res = Array.new
  res << :tgp_2010_production if bit? fld, 0b100_0000
  res << :tgp_validated       if bit? fld, 0b010_0000
  res << :tgp_2010_pilot      if bit? fld, 0b001_0000
  res << :tgp_2009_phase1     if bit? fld, 0b000_1000
  res << :phase_3_genotyped   if bit? fld, 0b000_0100
  res << :phase_2_genotyped   if bit? fld, 0b000_0010
  res << :phase_1_genotyped   if bit? fld, 0b000_0001
  res
end

#variation_class ⇒ Object

field F8



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# File 'lib/bio/ncbi/dbsnp/bitfield.rb', line 148

def variation_class
  case (field(8) & 0b0000_1111)
  when 0b0001
    :snp
  when 0b0010
    :dips
  when 0b0011
    :heterozygous
  when 0b0100
    :microsatellite
  when 0b0101
    :named_variation
  when 0b0110
    :novariation
  when 0b0111
    :mixed_class
  when 0b1000
    :multibase_polymorphism
  else
    raise "Should not happen! Check bitfield verison."
  end
end

#version ⇒ Object

field F0



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# File 'lib/bio/ncbi/dbsnp/bitfield.rb', line 36

def version
  field(0) & 0b0000_1111
end