Module: Exodb::Utils

Defined in:
lib/exodb/utils.rb,
lib/exodb/rositza.rb,
lib/exodb/rositza/load.rb,
lib/exodb/utils/upload_var.rb,
lib/exodb/utils/upload_generef.rb

Class Method Summary collapse

Class Method Details

.guess_miriam(str) ⇒ String

Guess the type of id

Parameters:

Returns:

  • (String) —

    a miriam registry or the string itself incase cannot guess



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# File 'lib/exodb/utils.rb', line 30

def guess_miriam(str)
  case str
  when /\A((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+|(NZ\_[A-Z]{4}\d+))(\.\d+)?\z/
    return "urn:miriam:refseq:#{str}"
  when /\A((ENS[A-Z]*[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))\z/
    return "urn:miriam:ensembl:#{str}"
  when /\A((HGNC|hgnc):)?\d{1,5}\z/
    return "urn:miriam:hgnc:#{str}"
  when /\ACCDS\d+\.\d+\z/
    return "urn:miriam:ccds:#{str}"
  else
    return str
  end
end

.load_indel_from_merge(mergefile) ⇒ Object 



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# File 'lib/exodb/rositza/load.rb', line 65

def load_indel_from_merge(mergefile)
  
  File.open(mergefile).each do |line|
    record = line.chomp.split("\t")
    p record[0..21]
    #others = record[22..-1]
    #until others.empty?
    # p others.shift(11)
    #end
  end
  
end

.load_sample_from_csv(csvfile) ⇒ Object 



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# File 'lib/exodb/rositza/load.rb', line 38

def load_sample_from_csv(csvfile)
  CSV.read(csvfile, col_sep: "\t", headers: true).each do |record|
    
    sample = Tumor.new({oid: record["SampleFinal"],
            type: record["Type"].downcase,
            typeid: "urn:miriam:bioportal.meddra:#{record["Type"] =~ /^spitz /i ? '10041632' : record["Type"] =~ /^spitzoid /i ? '10072450' : '10028679'}",
            patient: record["SampleFinal"].split('T')[0],
            preferred: record["Preferred"] == 'Y' ? true : false,
            paired: record["merge41final"] =~ /\Apaired\z/i ? true : false},
            labels: {})
    
    sample.add_to_dataset('internal.ds:000001')
    
    p sample.save!
    
  end
end

.load_variant_from_ann(annfile) ⇒ Object 



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# File 'lib/exodb/rositza/load.rb', line 56

def load_variant_from_ann(annfile)
  
  File.open(annfile).each do |line|
    record = line.chomp.split("\t")
    p record
  end
  
end

.load_variant_from_csv(csvfile) ⇒ Object 



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# File 'lib/exodb/rositza/load.rb', line 20

def load_variant_from_csv(csvfile)
  
  CSV.read(csvfile, col_sep: "\t", headers: true).each do |record|
    
    var = SNV.new()
    var.parse_location("#{record["chromosome"]}:#{record["start position"]}")
    var.reference = record["ref nucleotide"].split('/')[0]
    var.alternate = record["var nucleotide"].split('/').uniq
    var.somaticStatus = record["Somatic Status"]
    var.reads = record["Reads"]
    var.predicted_damage = record["PolyPhen"] =~ /probably_damaging/ || record["SIFT"] =~ /deleterious/i || record["PROVEAN"] =~ /deleterious/i ? true : false
    var.aachange = record["AA Change"]
    var.add_to_sample(record["cell"])
    
    p var.save!
  end
end

.load_variant_from_merge(mergefile) ⇒ Object 



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# File 'lib/exodb/rositza/load.rb', line 78

def load_variant_from_merge(mergefile)
  
  File.open(mergefile).each do |line|
    record = line.chomp.split("\t")
    
    header = record[0..15]
    
    list = record[16..-1]
    
    until list.empty?
      
      sampledata = list.shift(7)
      snvq = Exodb::Variant.where(oid: "#{header[2]}:#{header[3]}:#{sampledata[0]}")
      if snvq.exists?
        snv = snvq.first
        snv.temp.push(header[0..6].join("\t"))
        p snv.save!
      else
        snv = Exodb::Variant.new()
        snv.parse_location("#{header[2]}:#{header[3]}..#{header[3]}")
        snv.reference = header[10]
        snv.pileupt = sampledata[6]
        snv.temp = [] if snv.temp == nil
        snv.temp.push(header[0..6].join("\t"))
        snv.add_to_sample(sampledata[0])
        p snv.save!
      end
    end
  end
  
end

.upload_generef_from_gff3(filename, assembly = nil) ⇒ Object

Upload gene information to database using gff3 and genome sequence fasta file

Parameters:

  • gff3 (String) —

    file

  • assembly (String) (defaults to: nil) —

    name [default: gff file name]



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# File 'lib/exodb/utils/upload_generef.rb', line 23

def upload_generef_from_gff3(filename, assembly = nil)
  
  gff = Bio::GFF::GFF3.new(File.open(filename).read)
  
  processDbxref = lambda do |str|
    case str
    when /^GeneID/
      return "urn:miriam:ncbigene:#{str.split(/:/)[1]}"
    when /^HGNC/
      return "urn:miriam:hgnc:#{str}"
    when /^HPRD/
      return "urn:miriam:hprd:#{str.split(/:/)[1]}"
    when /^miRBase/
      return "urn:miriam:mirbase:#{str.split(/:/)[1]}"
    when /^Genbank/
      return "urn:miriam:refseq:#{str.split(/:/)[1]}"
    when /^CCDS/
      return "urn:miriam:ccds:#{str.split(/:/)[1]}"
    when /^MIM/
      return "urn:miriam:omim:#{str.split(/:/)[1]}"
    else
      return str
    end
  end
  
  assembly = assembly ? assembly : File.basename(filename, '.gff3')
  
  regions = {}
  genes = {}
  seq = {}
  
  
  gff.records.each do |e|
    
    case e.feature
    when 'region'
      e.attributes.each do |attr|
        case attr[0]
        when 'chromosome'
          regions[e.seqname] = attr[1] == 'X' ? 23 : attr[1] == 'Y' ? 24 : attr[1].to_i
        end
      end
      
      if File.exist?("./genome/#{e.seqname}.fa")
        seq = {}
        Bio::FlatFile.open(Bio::FastaFormat, "./genome/#{e.seqname}.fa").each {|fasta| seq[fasta.acc_version] = fasta.to_seq}
      end
      
    when 'gene', 'tRNA'
      
      gene = {type: 'gene', xrefs: [], strand: e.strand, chrrefseq: "#{guess_miriam(e.seqname)}", location: "#{e.seqname =~ /\ANC_/ ? regions[e.seqname] : e.seqname}:#{e.start}..#{e.end}", childs: [], exon: [], cds: []}
      
      e.attributes.each do |attr|
        case attr[0]
        when 'Dbxref'
          gene[:xrefs].push(processDbxref.call(attr[1]))
        when 'Name'
          gene[:xrefs].push("urn:miriam:hgnc.symbol:#{attr[1]}") if attr[1] !~ /^LOC\d+$/
        when 'pseudo'
          gene[:psuedo] = attr[1] == 'true' ? true : false
        when 'ID'
          gene[:id] = attr[1]
        end
      end
      
      gene[:sequence] = seq[e.seqname].subseq(e.start.to_i, e.end.to_i).to_s if seq.has_key?(e.seqname)
      gene[:oid] = gene[:location]
      genes[gene[:id]] = gene
      
    when /\A(transcript|[^t]*RNA)/
      rna = {type: 'rna', xrefs: [], strand: e.strand, chr: regions[e.seqname], location: "#{regions[e.seqname]}:#{e.start}..#{e.end}", exon: [], cds: []}
      
      e.attributes.each do |attr|
        case attr[0]
        when 'Dbxref'
          rna[:xrefs].push(processDbxref.call(attr[1]))
        when 'pseudo'
          rna[:psuedo] = attr[1] == 'true' ? true : false
        when 'ID'
          rna[:id] = attr[1]
        when 'Parent'
          rna[:parent] = attr[1]
        end
      end
      
      genes[rna[:id]] = rna
      genes[rna[:parent]][:childs].push(rna[:id]) if rna[:parent]
      
    when 'exon'
      e.attributes.each do |attr|
        case attr[0]
        when 'Parent'
          genes[attr[1]][:exon].push([e.start, e.end].sort)
        end
      end
    when 'CDS'
      e.attributes.each do |attr|
        case attr[0]
        when 'Parent'
          genes[attr[1]][:cds].push([e.start, e.end].sort)
        end
      end
    end
  end
  
  genes.each_pair do |k, v|
    if v[:type] == 'gene'
      
      gene = Generef.new()
      gene.oid = v[:oid] if v.has_key?(:oid)
      gene.xrefs = v[:xrefs]
      gene.parse_location(v[:location])
      gene.chrrefseq = v[:chrrefseq]
      gene.strand = v[:strand]
      gene.psuedo = v[:psuedo] if v[:psuedo]
      gene.genomeref = assembly
      gene.sequence = v[:sequence] if v.has_key?(:sequence)
      
      v[:childs].each do |child|
        
        rna = Isoform.new()
        data = genes[child]
        rna.xrefs = data[:xrefs]
        rna.exon = data[:exon].sort
        rna.cds = data[:cds].sort
        
        gene.isoforms.push(rna)
        
      end
      
      puts "STATUS: #{gene.save! ? "SUCCESS" : "FAIL"}: Deposit Gene reference #{gene.xrefs[0]}"
      
    end
    
  end
  
  
end