Class: Bio::FastQC::Semantics

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/fastqc/semantics.rb

Instance Method Summary collapse

Constructor Details

#initialize(fastqc_object, id: nil, runid: nil, tiny: true) ⇒ Semantics

Returns a new instance of Semantics.



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# File 'lib/bio/fastqc/semantics.rb', line 9

def initialize(fastqc_object, id: nil, runid: nil, tiny: true)
  @id = id
  @runid = runid
  @tiny = tiny
  @fastqc_object = fastqc_object
end

Instance Method Details

#adapter_content ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 498

def adapter_content
  {}
end

#base_stat_class(base) ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 137

def base_stat_class(base)
  case base
  when /-/ # when the base position is range like "50-100"
    "BaseRangeStatistics"
  else
    "ExactBaseStatistics"
  end
end

#encoding ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 164

def encoding
  {
    "encoding" => @fastqc_object[:encoding],
  }
end

#fastqc_version ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 146

def fastqc_version
  {
    "fastqcVersion" => @fastqc_object[:fastqc_version],
  }
end

#file_type ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 158

def file_type
  {
    "fileType" => @fastqc_object[:file_type],
  }
end

#filename ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 152

def filename
  {
    "filename" => @fastqc_object[:filename],
  }
end

#filtered_sequences ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 181

def filtered_sequences
  {
    "@type" => "filteredSequences",
    "sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
    "sio:SIO_000300" => {
      "@value" => @fastqc_object[:filtered_sequences],
      "@type" => "xsd:integer",
    }
  }
end

#identifier_literal ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 59

def identifier_literal
  @id ? @id : "QNT_" + @fastqc_object[:filename].split(".")[0]
end

#identifier_uri ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 63

def identifier_uri
  "quanto:" + identifier_literal
end

#json_ld_object ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 43

def json_ld_object
  object = [object_core, static_value_modules, object_modules].flatten.inject(&:merge)
  if !@tiny
    object["hasMatrix"] = matrix_modules
  end
  object
end

#jsonld_context ⇒ Object

Generate JSON-LD context object



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# File 'lib/bio/fastqc/semantics.rb', line 621

def jsonld_context
  # definition of imported terms in @context
  object = turtle_prefixes

  # definition of local ontology terms
  pfx = "sos:"

  # definition of class in @context
  sos_class.each do |term|
    object[term] = {}
    object[term]["@id"] = pfx + term
    object[term]["@type"] = "@id"
  end

  # definition of object properties in @context
  sos_object_properties.each do |term|
    object[term] = {}
    object[term]["@id"] = pfx + term
    object[term]["@type"] = "@id"
  end

  sos_data_properties_string.each do |term|
    object[term] = {}
    object[term]["@id"] = pfx + term
    object[term]["@type"] = "http://www.w3.org/2001/XMLSchema#string"
  end

  sos_data_properties_integer.each do |term|
    object[term] = {}
    object[term]["@id"] = pfx + term
    object[term]["@type"] = "http://www.w3.org/2001/XMLSchema#integer"
  end

  sos_data_properties_float.each do |term|
    object[term] = {}
    object[term]["@id"] = pfx + term
    object[term]["@type"] = "http://www.w3.org/2001/XMLSchema#float"
  end

  object
end

#kmer_content ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 502

def kmer_content
  {
    "@type" => "KmerContent",
    "hasRow" => kmer_content_rows(@fastqc_object[:kmer_content]),
  }
end

#kmer_content_rows(matrix) ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 509

def kmer_content_rows(matrix)
  matrix.map.with_index do |row, i|
    sequence = row[0]
    count = row[1]
    ratio_overall = row[2]
    ratio_max = row[3]
    ratio_max_position = row[4]
    {
      "@type" => "Row",
      "rowIndex" => i,
      "kmerSequence" => sequence,
      "sequenceReadCount" => {
        "@type" => "SequenceReadAmount",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
        "sio:SIO_000300" => count,
      },
      "observedPerExpectedOverall" => {
        "@type" => "SequenceReadAmount",
        "sio:SIO_000221" => { "@id" => "obo:Ratio" },
        "sio:SIO_000300" => ratio_overall,
      },
      "observedPerExpectedMax" => {
        "@type" => "SequenceReadAmount",
        "sio:SIO_000221" => { "@id" => "obo:Ratio" },
        "sio:SIO_000300" => ratio_max,
      },
      "observedPerExpectedMaxPosition" => ratio_max_position,
    }
  end
end

#matrix_modules ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 121

def matrix_modules
  [
    per_base_sequence_quality,
    per_tile_sequence_quality,
    per_sequence_quality_scores,
    per_base_sequence_content,
    per_sequence_gc_content,
    per_base_n_content,
    sequence_length_distribution,
    sequence_duplication_levels,
    overrepresented_sequences,
    adapter_content,
    kmer_content,
  ]
end

#max_length ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 551

def max_length
  {
    "@type" => "maxSequenceLength",
    "sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
    "sio:SIO_000300" => {
      "@value" => @fastqc_object[:max_length],
      "@type" => "xsd:integer",
    },
  }
end

#mean_sequence_length ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 562

def mean_sequence_length
  {
    "@type" => "meanSequenceLength",
    "sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
    "sio:SIO_000300" => {
      "@value" => @fastqc_object[:mean_sequence_length],
      "@type" => "xsd:decimal",
    },
  }
end

#median_sequence_length ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 573

def median_sequence_length
  {
    "@type" => "medianSequenceLength",
    "sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
    "sio:SIO_000300" => {
      "@value" => @fastqc_object[:median_sequence_length],
      "@type" => "xsd:decimal",
    },
  }
end

#min_length ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 540

def min_length
  {
    "@type" => "minimumSequenceLength",
    "sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
    "sio:SIO_000300" => {
      "@value" => @fastqc_object[:min_length],
      "@type" => "xsd:integer",
    },
  }
end

#object_core ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 67

def object_core
  {
    "@context" => jsonld_context,
    "@id" => identifier_uri,
    "@type" => "SequenceStatisticsReport",
    "dcterms:identifier" => identifier_literal,
    "dcterms:contributor" => ["Tazro Ohta", "Shuichi Kawashima"],
    "dcterms:created" => {
      "@value" => Time.now.strftime("%Y-%m-%d"),
      "@type" => "xsd:date"
    },
    "dcterms:license" => {
      "@id" => "http://creativecommons.org/licenses/by-sa/4.0/",
    },
    "dcterms:publisher" => {
      "@id" => "http://dbcls.rois.ac.jp/",
    },
    "pav:version" => rdf_version,
    "foaf:page" => {
      "@id" => "http://quanto.dbcls.jp",
    },
    "rdfs:seeAlso" => {
      "@id" => "http://identifiers.org/insdc.sra/" + sra_identifier,
    },
  }
end

#object_modules ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 103

def object_modules
  {
    "sio:SIO_000216" => [
      total_sequences,
      filtered_sequences,
      percent_gc,
      #total_duplicate_percentage,
      min_length,
      max_length,
      overall_mean_quality_score,
      overall_median_quality_score,
      overall_n_content,
      mean_sequence_length,
      median_sequence_length,
    ]
  }
end

#overall_mean_quality_score ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 584

def overall_mean_quality_score
  {
    "@type" => "meanBaseCallQuality",
    "sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
    "sio:SIO_000300" => {
      "@value" => @fastqc_object[:overall_mean_quality_score],
      "@type" => "xsd:decimal",
    },
  }
end

#overall_median_quality_score ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 595

def overall_median_quality_score
  {
    "@type" => "medianBaseCallQuality",
    "sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
    "sio:SIO_000300" => {
      "@value" => @fastqc_object[:overall_median_quality_score],
      "@type" => "xsd:decimal",
    },
  }
end

#overall_n_content ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 606

def overall_n_content
  {
    "@type" => "nContent",
    "sio:SIO_000221" => { "@id" => "obo:UO_0000187" },
    "sio:SIO_000300" => {
      "@value" => @fastqc_object[:overall_n_content],
      "@type" => "xsd:decimal",
    },
  }
end

#overrepresented_sequences ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 466

def overrepresented_sequences
  {
    "@type" => "OverrepresentedSequences",
    "hasRow" => overrepresented_sequences_rows(@fastqc_object[:overrepresented_sequences]),
  }
end

#overrepresented_sequences_rows(matrix) ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 473

def overrepresented_sequences_rows(matrix)
  matrix.map.with_index do |row, i|
    sequence = row[0]
    count = row[1]
    percentage = row[2]
    possible_source = row[3]
    {
      "@type" => "Row",
      "rowIndex" => i,
      "overrepresentedSequence" => sequence,
      "sequenceReadCount" => {
        "@type" => "SequenceReadAmount",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
        "sio:SIO_000300" => count,
      },
      "sequenceReadPercentage" => {
        "@type" => "SequenceReadRatio",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000187" },
        "sio:SIO_000300" => percentage,
      },
      "possibleSourceOfSequence" => possible_source,
    }
  end
end

#per_base_n_content ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 377

def per_base_n_content
  {
    "@type" => "PerBaseNContent",
    "hasRow" => per_base_n_content_rows(@fastqc_object[:per_base_n_content]),
  }
end

#per_base_n_content_rows(matrix) ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 384

def per_base_n_content_rows(matrix)
  matrix.map.with_index do |row, i|
    base = row[0]
    n_count = row[1]
    {
      "@type" => [
        "Row",
        base_stat_class(base),
      ],
      "rowIndex" => i,
      "basePosition" => base,
      "nCount" => {
        "@type" => "BaseRatio",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000187" },
        "sio:SIO_000300" => n_count,
      },
    }
  end
end

#per_base_sequence_content ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 304

def per_base_sequence_content
  {
    "@type" => "PerBaseSequenceContent",
    "hasRow" => per_base_sequence_content_rows(@fastqc_object[:per_base_sequence_content]),
  }
end

#per_base_sequence_content_rows(matrix) ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 311

def per_base_sequence_content_rows(matrix)
  matrix.map.with_index do |row, i|
    base = row[0]
    guanine = row[1]
    adenine = row[2]
    thymine = row[3]
    chytosine = row[4]
    {
      "@type" => [
        "Row",
        base_stat_class(base),
      ],
      "rowIndex" => i,
      "basePosition" => base,
      "percentGuanine" => {
        "@type" => "BaseRatio",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000187" },
        "sio:SIO_000300" => guanine,
      },
      "percentAdenine" => {
        "@type" => "BaseRatio",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000187" },
        "sio:SIO_000300" => adenine,
      },
      "percentThymine" => {
        "@type" => "BaseRatio",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000187" },
        "sio:SIO_000300" => thymine,
      },
      "percentCytosine" => {
        "@type" => "BaseRatio",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000187" },
        "sio:SIO_000300" => chytosine,
      },
    }
  end
end

#per_base_sequence_quality ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 214

def per_base_sequence_quality
  {
    "@type" => "PerBaseSequenceQuality",
    "hasRow" => per_base_sequence_quality_rows(@fastqc_object[:per_base_sequence_quality]),
  }
end

#per_base_sequence_quality_rows(matrix) ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 221

def per_base_sequence_quality_rows(matrix)
  matrix.map.with_index do |row, i|
    base = row[0]
    mean = row[1]
    median = row[2]
    lower_quartile = row[3]
    upper_quartile = row[4]
    tenth_percentile = row[5]
    ninetieth_percentile = row[6]

    {
      "@type" => [
        "Row",
        base_stat_class(base),
      ],
      "rowIndex" => i,
      "basePosition" => base,
      "meanBaseCallQuality" => {
        "@type" => "PhredQualityScore",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
        "sio:SIO_000300" => mean,
      },
      "medianBaseCallQuality" => {
        "@type" => "PhredQualityScore",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
        "sio:SIO_000300" => median,
      },
      "baseCallQualityLowerQuartile" => {
        "@type" => "PhredQualityScore",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
        "sio:SIO_000300" => lower_quartile,
      },
      "baseCallQualityUpperQuartile" => {
        "@type" => "PhredQualityScore",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
        "sio:SIO_000300" => upper_quartile,
      },
      "baseCallQuality10thPercentile" => {
        "@type" => "PhredQualityScore",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
        "sio:SIO_000300" => tenth_percentile,
      },
      "baseCallQuality90thPercentile" => {
        "@type" => "PhredQualityScore",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
        "sio:SIO_000300" => ninetieth_percentile,
      },
    }
  end
end

#per_sequence_gc_content ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 349

def per_sequence_gc_content
  {
    "@type" => "PerSequenceGCContent",
    "hasRow" => per_sequence_gc_content_rows(@fastqc_object[:per_sequence_gc_content]),
  }
end

#per_sequence_gc_content_rows(matrix) ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 356

def per_sequence_gc_content_rows(matrix)
  matrix.map.with_index do |row, i|
    gc_content = row[0]
    count = row[1]
    {
      "@type" => "Row",
      "rowIndex" => i,
      "percentGC" => {
        "@type" => "BaseRatio",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000187" },
        "sio:SIO_000300" => gc_content,
      },
      "sequenceReadCount" => {
        "@type" => "SequenceReadAmount",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
        "sio:SIO_000300" => count,
      },
    }
  end
end

#per_sequence_quality_scores ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 276

def per_sequence_quality_scores
  {
    "@type" => "PerSequnceQualityScores",
    "hasRow" => per_sequence_quality_scores_rows(@fastqc_object[:per_sequence_quality_scores]),
  }
end

#per_sequence_quality_scores_rows(matrix) ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 283

def per_sequence_quality_scores_rows(matrix)
  matrix.map.with_index do |row, i|
    quality = row[0]
    count = row[1]
    {
      "@type" => "Row",
      "rowIndex" => i,
      "baseCallQuality" => {
        "@type" => "PhredQualityScore",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
        "sio:SIO_000300" => quality,
      },
      "sequenceReadCount" => {
        "@type" => "SequenceReadAmount",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
        "sio:SIO_000300" => count,
      },
    }
  end
end

#per_tile_sequence_quality ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 272

def per_tile_sequence_quality
  {}
end

#percent_gc ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 203

def percent_gc
  {
    "@type" => "percentGC",
    "sio:SIO_000221" => { "@id" => "obo:UO_0000187" },
    "sio:SIO_000300" => {
      "@value" => @fastqc_object[:percent_gc],
      "@type" => "xsd:decimal",
    }
  }
end

#rdf_version ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 16

def rdf_version
  "0.2.0"
end

#sequence_duplication_levels ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 437

def sequence_duplication_levels
  {
    "@type" => "SequenceDuplicationLevels",
    "hasRow" => sequence_duplication_levels_rows(@fastqc_object[:sequence_duplication_levels]),
  }
end

#sequence_duplication_levels_rows(matrix) ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 444

def sequence_duplication_levels_rows(matrix)
  matrix.map.with_index do |row, i|
    duplication_level = row[0]
    relative_count = row[1]
    {
      "@type" => "Row",
      "rowIndex" => i,

      "sequenceDuplicationLevel" => {
        "@type" => "SequenceDuplicationLevel",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
        "sio:SIO_000300" => duplication_level,
      },
      "sequenceReadRelativeCount" => {
        "@type" => "SequenceReadAmount",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
        "sio:SIO_000300" => relative_count,
      },
    }
  end
end

#sequence_length ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 192

def sequence_length
  {
    "@type" => "SequenceReadLength",
    "sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
    "sio:SIO_000300" => {
      "@value" => @fastqc_object[:sequence_length],
      "@type" => "xsd:string",
    }
  }
end

#sequence_length_distribution ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 404

def sequence_length_distribution
  {
    "@type" => "SequenceLengthDistribution",
    "hasRow" => sequence_length_distribution_rows(@fastqc_object[:sequence_length_distribution]),
  }
end

#sequence_length_distribution_rows(matrix) ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 411

def sequence_length_distribution_rows(matrix)
  matrix.map.with_index do |row, i|
    length = row[0]
    count = row[1]
    {
      "@type" => "Row",
      "rowIndex" => i,

      "sequenceReadLength" => {
        "@type" => "SequenceReadLength",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
        "sio:SIO_000300" => length,
      },
      "sequenceReadCount" => {
        "@type" => "SequenceReadAmount",
        "sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
        "sio:SIO_000300" => count,
      },
    }
  end
end

#sos_class ⇒ Object

definition of classes



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# File 'lib/bio/fastqc/semantics.rb', line 667

def sos_class
  [
    sos_class_general,
    sos_class_fastqc_modules,
    sos_class_for_values,
  ].flatten
end

#sos_class_fastqc_modules ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 685

def sos_class_fastqc_modules
  [
    "PerBaseSequenceQuality",
    "PerTileSequenceQuality",
    "PerSequnceQualityScores",
    "PerBaseSequenceContent",
    "PerSequenceGCContent",
    "PerBaseNContent",
    "SequenceLengthDistribution",
    "SequenceDuplicationLevels",
    "OverrepresentedSequences",
    "KmerContent",
  ]
end

#sos_class_for_values ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 700

def sos_class_for_values
  [
    "PhredQualityScore",
    "BaseRatio",
    "SequenceReadAmount",
    "SequenceReadRatio",
    "SequenceReadLength",
    "SequenceDuplicationLevel",
    "nContent",
    "percentGC",
    "medianBaseCallQuality",
    "meanBaseCallQuality",
    "totalSequences",
    "filteredSequences",
    "minimumSequenceLength",
    "maxSequenceLength",
    "meanSequenceLength",
    "medianSequenceLength",
  ]
end

#sos_class_general ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 675

def sos_class_general
  [
    "SequenceStatisticsReport",
    "SequenceStatisticsMatrix",
    "Row",
    "ExactBaseStatistics",
    "BaseRangeStatistics",
  ]
end

#sos_data_properties_float ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 774

def sos_data_properties_float
  [
    "baseCallQuality",
    "baseCallQuality10thPercentile",
    "baseCallQuality90thPercentile",
    "baseCallQualityLowerQuartile",
    "baseCallQualityUpperQuartile",
    "minSequenceLength",
    "maxSequenceLength",
    "meanSequenceLength",
    "medianSequenceLength",
  ]
end

#sos_data_properties_integer ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 768

def sos_data_properties_integer
  [
    "rowIndex",
  ]
end

#sos_data_properties_string ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 757

def sos_data_properties_string
  [
    "fastqcVersion",
    "filename",
    "fileType",
    "encoding",
    "possibleSourceOfSequence",
    "overrepresentedSequence",
  ]
end

#sos_object_properties ⇒ Object

definition of predicates



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# File 'lib/bio/fastqc/semantics.rb', line 725

def sos_object_properties
  [
    "hasMatrix",
    "totalSequences",
    "filteredSequences",
    "sequenceLength",
    "percentGC",
    "hasRow",
    "basePosition",
    "kmerSequence",
    "meanBaseCallQuality",
    "medianBaseCallQuality",
    "nCount",
    "observedPerExpectedMax",
    "observedPerExpectedMaxPosition",
    "observedPerExpectedOverall",
    "percentAdenine",
    "percentCytosine",
    "percentGC",
    "percentGuanine",
    "percentThymine",
    "sequenceDuplicationLevel",
    "sequenceReadCount",
    "sequenceReadLength",
    "sequenceReadPercentage",
    "sequenceReadRelativeCount",
    "overallMeanBaseCallQuality",
    "overallMedianBaseCallQuality",
    "overallNContent",
  ]
end

#sra_identifier ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 55

def sra_identifier
  @runid ? @runid : @fastqc_object[:filename].split(".")[0].split("_")[0]
end

#static_value_modules ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 94

def static_value_modules
  [
    fastqc_version,
    filename,
    file_type,
    encoding,
  ]
end

#total_duplicate_percentage ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 433

def total_duplicate_percentage
  {}
end

#total_sequences ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 170

def total_sequences
  {
    "@type" => "totalSequences",
    "sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
    "sio:SIO_000300" => {
      "@value" => @fastqc_object[:total_sequences],
      "@type" => "xsd:integer",
    },
  }
end

#turtle ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 20

def turtle
  turtle_graph.dump(:ttl, prefixes: turtle_prefixes)
end

#turtle_graph ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 24

def turtle_graph
  RDF::Graph.new << JSON::LD::API.toRdf(json_ld_object)
end

#turtle_prefixes ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 28

def turtle_prefixes
  {
    "obo" => "http://purl.obolibrary.org/obo/",
    "rdf" => "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
    "rdfs" => "http://www.w3.org/2000/01/rdf-schema#",
    "dcterms" => "http://purl.org/dc/terms/",
    "pav" => "http://purl.org/pav/",
    "foaf" => "http://xmlns.com/foaf/0.1/",
    "sos" => "http://purl.jp/bio/10/quanto/ontology/sos#",
    "quanto" => "http://purl.jp/bio/10/quanto/resource/",
    "sio" => "http://semanticscience.org/resource/",
    "xsd" => "http://www.w3.org/2001/XMLSchema#",
  }
end

#uri_base ⇒ Object 



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# File 'lib/bio/fastqc/semantics.rb', line 51

def uri_base
  "http://purl.jp/bio/01/quanto"
end