Class: PubliSci::Generators::MAF

Inherits:
Object
  • Object
show all
Extended by:
Base
Defined in:
lib/publisci/generators/maf.rb

Constant Summary collapse

COLUMN_NAMES = 
%w{ Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS  dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1  Match_Norm_Seq_Allele2  Tumor_Validation_Allele1  Tumor_Validation_Allele2  Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase  Sequence_Source Validation_Method Score BAM_File  Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID patient_id sample_id}
COMPONENT_RANGES = 
{ "Tumor_Sample_Barcode" => "xsd:string", "Start_position" => "xsd:int", "Center" => "xsd:string", "NCBI_Build" => "xsd:int", "Chromosome" => "xsd:int" }
TCGA_CODES = 
{
  "Variant_Classification" => %w{Frame_Shift_Del Frame_Shift_Ins In_Frame_Del In_Frame_Ins Missense_Mutation Nonsense_Mutation Silent Splice_Site Translation_Start_Site Nonstop_Mutation 3'UTR 3'Flank 5'UTR 5'Flank IGR1  Intron RNA Targeted_Region},
  "Variant_Type" => %w{SNP DNP TNP ONP INS DEL Consolidated},
  "dbSNP_Val_Status" => %w{by1000genomes by2Hit2Allele byCluster byFrequency byHapMap byOtherPop bySubmitter alternate_allele},
  "Verification_Status" => %w{Verified, Unknown},
  "Validation_Status" => %w{Untested Inconclusive Valid Invalid},
  "Mutation_Status" => %w{None Germline Somatic LOH Post-transcriptional modification Unknown},
  "Sequence_Source" => %w{WGS WGA WXS RNA-Seq miRNA-Seq Bisulfite-Seq VALIDATION Other ncRNA-Seq WCS CLONE POOLCLONE AMPLICON CLONEEND FINISHING ChIP-Seq MNase-Seq DNase-Hypersensitivity EST FL-cDNA CTS MRE-Seq MeDIP-Seq MBD-Seq Tn-Seq FAIRE-seq SELEX RIP-Seq ChIA-PET},
  "Sequencer" => ["Illumina GAIIx", "Illumina HiSeq", "SOLID", "454", "ABI 3730xl", "Ion Torrent PGM", "Ion Torrent Proton", "PacBio RS", "Illumina MiSeq", "Illumina HiSeq 2500", "454 GS FLX Titanium", "AB SOLiD 4 System" ]
}
BARCODE_INDEX = 
COLUMN_NAMES.index('Tumor_Sample_Barcode')

Class Method Summary collapse

Methods included from Base

close_output, write, write_to

Methods included from Dataset::DataCube

#abbreviate_known, #code_lists, #component_gen, #component_specifications, #concept_codes, #data_structure_definition, #dataset, #defaults, #dimension_properties, #encode_data, #generate, #generate_resources, #measure_properties, #observations, #prefixes, #vocabulary

Methods included from RDFParser

#add_node, #bnode_value, #encode_value, #get_ary, #get_hashes, #is_complex?, #is_uri?, #load_string, #observation_hash, #sanitize, #sanitize_hash, #strip_prefixes, #strip_uri, #to_literal, #to_resource, #turtle_indent

Class Method Details

.column_replace(entry, column, prefix, value = nil) ⇒ Object 



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# File 'lib/publisci/generators/maf.rb', line 140

def column_replace(entry,column,prefix,value=nil)
  if value
    entry[COLUMN_NAMES.index(column)] = prefix + value
  else
    entry[COLUMN_NAMES.index(column)] += prefix
  end
end

.official_symbol(hugo_symbol) ⇒ Object 



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# File 'lib/publisci/generators/maf.rb', line 148

def official_symbol(hugo_symbol)
  qry = <<-EOF

  SELECT distinct ?official where {
   {?hgnc <http://bio2rdf.org/hgnc_vocabulary:approved_symbol> "#{hugo_symbol}"}
   UNION
   {?hgnc <http://bio2rdf.org/hgnc_vocabulary:synonym> "#{hugo_symbol}"}

   ?hgnc <http://bio2rdf.org/hgnc_vocabulary:approved_symbol> ?official
  }

  EOF

  sparql = SPARQL::Client.new("http://cu.hgnc.bio2rdf.org/sparql")
  sparql.query(qry).map(&:official).first.to_s
end

.parse_barcode(code) ⇒ Object 



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# File 'lib/publisci/generators/maf.rb', line 165

def parse_barcode(code)
  #TCGA-E9-A22B-01A-11D-A159-09
  [code[5..11], code[13..-1]]
end

.post_process(file) ⇒ Object 



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# File 'lib/publisci/generators/maf.rb', line 131

def post_process(file)
  reg = %r{http://identifiers.org/hgnc.symbol/(\w+)}
  hugo_cache ||= {}
  PubliSci::PostProcessor.process(file,file,reg){|g|
    hugo_cache[g] ||= official_symbol(g)
   'http://identifiers.org/hgnc.symbol/' + cache[g]
 }
end

.process_line(entry, label, options) ⇒ Object 



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# File 'lib/publisci/generators/maf.rb', line 50

def process_line(entry,label,options)
    entry = (entry.fill(nil,entry.length...COLUMN_NAMES.length-2) + parse_barcode(entry[BARCODE_INDEX])).flatten

    entry[0] = "http://identifiers.org/hgnc.symbol/#{entry[0]}" if entry[0]

    # A 0 in the entrez-id column appears to mean null
    col=1
    entry[col] = nil if entry[col] == '0'
    entry[col] = "http://identifiers.org/ncbigene/#{entry[col]}" if entry[col]

    # Only link non-novel dbSNP entries
    col = COLUMN_NAMES.index('dbSNP_RS')
    if entry[col] && entry[col][0..1] == "rs"
      entry[col] = "http://identifiers.org/dbsnp/#{entry[col].gsub('rs','')}"
    end

    # optionally create typed objects using sio nodes
    if options[:complex_objects]
      entry = sio_values(entry)
    end

    data = {}
    COLUMN_NAMES.each_with_index{|col,i|
      data[col] = [entry[i]]
    }

    observations(options[:measures],options[:dimensions],options[:codes],data,[label],options[:dataset_name],options).first
end

.process_options(options) ⇒ Object 



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# File 'lib/publisci/generators/maf.rb', line 41

def process_options(options)
  options[:dimensions] = dimensions = %w{Variant_Classification Variant_Type dbSNP_Val_Status Verification_Status Validation_Status Mutation_Status Sequence_Source Sequencer}
  options[:codes] = codes = dimensions
  options[:measures] = (COLUMN_NAMES - dimensions - codes)
  options[:dataset_name] ||= "MAF_#{Time.now.nsec.to_s(32)}"

  options
end

.sio_values(entry) ⇒ Object 



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# File 'lib/publisci/generators/maf.rb', line 79

def sio_values(entry)
  entry[0] = sio_value('http://edamontology.org/data_1791',entry[0]) if entry[0]

  # Link entrez genes
  col=1
  entry[col] = sio_value("http://identifiers.org/ncbigene",entry[col]) if entry[col]

  col = COLUMN_NAMES.index('dbSNP_RS')
  entry[col] = sio_value("http://identifiers.org/dbsnp", entry[col])

  # test SIO attributes for chromosome
  col = COLUMN_NAMES.index('Chromosome')
  entry[col] = sio_value("http://purl.org/obo/owl/SO#SO_0000340",entry[col])

  # More SIO attrtibutes for alleles
  %w{Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2}.each{|name|
    col = COLUMN_NAMES.index(name)
    entry[col] = sio_value("http://purl.org/obo/owl/SO#SO_0001023",entry[col])
  }

  col = COLUMN_NAMES.index("Strand")
  entry[col] = sio_attribute("http://edamontology.org/data_0853",entry[col])

  col = COLUMN_NAMES.index("Center")
  entry[col] = sio_attribute("foaf:homepage",entry[col])

  # Use faldo for locations End_Position
  col = COLUMN_NAMES.index("Start_Position")
  entry[col] = sio_attribute("http://biohackathon.org/resource/faldo#begin", entry[col],"http://biohackathon.org/resource/faldo#Position")

  col = COLUMN_NAMES.index("End_Position")
  entry[col] = sio_attribute("http://biohackathon.org/resource/faldo#end", entry[col],"http://biohackathon.org/resource/faldo#Position")

  entry
end

.structure(options = {}) ⇒ Object 



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# File 'lib/publisci/generators/maf.rb', line 115

def structure(options={})

  options = process_options(options)

  str = prefixes(options[:dataset_name],options)
  str << data_structure_definition(options[:measures],options[:dimensions],options[:codes],options[:dataset_name],options)
  str << dataset(options[:dataset_name],options)
  component_specifications(options[:measures], options[:dimensions], options[:codes], options[:dataset_name], options).map{ |c| str << c }
  measure_properties(options[:measures],options[:dataset_name],options).map{|m| str << m}
  dimension_properties(options[:dimensions],options[:codes], options[:dataset_name],options).map{|d| str << d}
  code_lists(options[:codes],TCGA_CODES,options[:dataset_name],options).map{|c| str << c}
  concept_codes(options[:codes],TCGA_CODES,options[:dataset_name],options).map{|c| str << c}

  str
end

.write(record, out, label, options = {}) ⇒ Object 



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# File 'lib/publisci/generators/maf.rb', line 25

def write(record, out, label, options={})

    options = process_options(options)

    options[:no_labels] ||= true
    options[:lookup_hugo] ||= false
    options[:complex_objects] ||= false
    options[:ranges] ||= COMPONENT_RANGES

    write_to(out, process_line(record, label, options))
end

.write_structure(input, output, options) ⇒ Object 



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# File 'lib/publisci/generators/maf.rb', line 37

def write_structure(input, output, options)
  write_to(output, structure(options))
end