bio-fastqc 0.6.0 → 0.7.0

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Files changed (4) hide show
  1. checksums.yaml +4 -4
  2. data/VERSION +1 -1
  3. data/lib/bio/fastqc/semantics.rb +26 -23
  4. metadata +2 -2
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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data/VERSION CHANGED
@@ -1 +1 @@
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- 0.6.0
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+ 0.7.0
data/lib/bio/fastqc/semantics.rb CHANGED
@@ -6,8 +6,9 @@ require 'rdf/turtle'
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  module Bio
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  module FastQC
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  class Semantics
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- def initialize(fastqc_object, id: nil)
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+ def initialize(fastqc_object, id: nil, tiny: true)
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  @id = id
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+ @tiny = tiny
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  @fastqc_object = fastqc_object
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  end
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@@ -35,7 +36,9 @@ module Bio
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  def json_ld_object
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  object = [object_core, static_value_modules].flatten.inject(&:merge)
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- object["hasMatrix"] = matrix_modules
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+ if !@tiny
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+ object["hasMatrix"] = matrix_modules
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+ end
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  object
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  end
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@@ -139,7 +142,7 @@ module Bio
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  def total_sequences
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  {
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  "totalSequences" => {
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- "@type" => "SequenceReadContent",
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+ "@type" => "SequenceReadAmount",
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  "hasUnit" => "uo:CountUnit",
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  "rdf:value" => @fastqc_object[:total_sequences],
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  }
@@ -149,7 +152,7 @@ module Bio
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  def filtered_sequences
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  {
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  "filteredSequences" => {
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- "@type" => "SequenceReadContent",
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+ "@type" => "SequenceReadAmount",
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  "hasUnit" => "uo:CountUnit",
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  "rdf:value" => @fastqc_object[:filtered_sequences],
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  }
@@ -169,7 +172,7 @@ module Bio
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  def percent_gc
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  {
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  "percentGC" => {
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- "@type" => "NucleotideBaseContent",
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+ "@type" => "SequenceBaseAmount",
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  "hasUnit" => "uo:CountUnit",
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  "rdf:value" => @fastqc_object[:percent_gc],
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  }
@@ -258,7 +261,7 @@ module Bio
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  "rdf:value" => quality,
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  },
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  "sequenceReadCount" => {
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- "@type" => "SequenceReadContent",
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+ "@type" => "SequenceReadAmount",
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  "hasUnit" => "uo:CountUnit",
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  "rdf:value" => count,
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  },
@@ -288,22 +291,22 @@ module Bio
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  "rowIndex" => i,
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  "basePosition" => base,
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  "percentGuanine" => {
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- "@type" => "NucleotideBaseContent",
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+ "@type" => "SequenceBaseAmount",
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  "hasUnit" => "uo:Percentage",
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  "rdf:value" => guanine,
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  },
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  "percentAdenine" => {
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- "@type" => "NucleotideBaseContent",
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+ "@type" => "SequenceBaseAmount",
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  "hasUnit" => "uo:Percentage",
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  "rdf:value" => adenine,
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  },
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  "percentThymine" => {
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- "@type" => "NucleotideBaseContent",
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+ "@type" => "SequenceBaseAmount",
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  "hasUnit" => "uo:Percentage",
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  "rdf:value" => thymine,
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  },
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  "percentCytosine" => {
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- "@type" => "NucleotideBaseContent",
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+ "@type" => "SequenceBaseAmount",
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  "hasUnit" => "uo:Percentage",
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  "rdf:value" => chytosine,
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  },
@@ -326,12 +329,12 @@ module Bio
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  "@type" => "Row",
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  "rowIndex" => i,
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  "percentGC" => {
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- "@type" => "NucleotideBaseContent",
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+ "@type" => "SequenceBaseAmount",
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  "hasunit" => "uo:Percent",
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  "rdf:value" => gc_content,
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  },
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  "sequenceReadCount" => {
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- "@type" => "SequenceReadContent",
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+ "@type" => "SequenceReadAmount",
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  "hasUnit" => "uo:CountUnit",
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  "rdf:value" => count,
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  },
@@ -358,7 +361,7 @@ module Bio
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  "rowIndex" => i,
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  "basePosition" => base,
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  "nCount" => {
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- "@type" => "NContent",
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+ "@type" => "SequenceBaseAmount",
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  "hasUnit" => "uo:Percentage",
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  "rdf:value" => n_count,
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  },
@@ -387,7 +390,7 @@ module Bio
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  "rdf:value" => length,
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  },
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  "sequenceReadCount" => {
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- "@type" => "SequenceReadContent",
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+ "@type" => "SequenceReadAmount",
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  "hasUnit" => "uo:CountUnit",
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  "rdf:value" => count,
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  },
@@ -420,7 +423,7 @@ module Bio
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  "rdf:value" => duplication_level,
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  },
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  "sequenceReadRelativeCount" => {
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- "@type" => "SequenceReadContent",
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+ "@type" => "SequenceReadAmount",
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  "hasUnit" => "uo:CountUnit",
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  "rdf:value" => relative_count,
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  },
@@ -446,12 +449,12 @@ module Bio
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  "rowIndex" => i,
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  "overrepresentedSequence" => sequence,
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  "sequenceReadCount" => {
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- "@type" => "SequenceReadContent",
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+ "@type" => "SequenceReadAmount",
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  "hasUnit" => "uo:CountUnit",
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  "rdf:value" => count,
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  },
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  "sequenceReadPercentage" => {
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- "@type" => "SequenceReadContent",
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+ "@type" => "SequenceReadAmount",
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  "hasUnit" => "uo:Percentage",
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  "rdf:value" => percentage,
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  },
@@ -483,17 +486,17 @@ module Bio
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  "rowIndex" => i,
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  "kmerSequence" => sequence,
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  "sequenceReadCount" => {
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- "@type" => "SequenceReadContent",
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+ "@type" => "SequenceReadAmount",
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  "hasUnit" => "uo:CountUnit",
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  "rdf:value" => count,
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  },
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  "observedPerExpectedOverall" => {
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- "@type" => "SequenceReadContent",
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+ "@type" => "SequenceReadAmount",
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  "hasUnit" => "uo:Ratio",
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  "rdf:value" => ratio_overall,
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  },
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  "observedPerExpectedMax" => {
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- "@type" => "SequenceReadContent",
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+ "@type" => "SequenceReadAmount",
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  "hasUnit" => "uo:Ratio",
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  "rdf:value" => ratio_max,
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  },
@@ -565,7 +568,7 @@ module Bio
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  def overall_n_content
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  {
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  "overallNContent" => {
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- "@type" => "NContent",
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+ "@type" => "SequenceBaseAmount",
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  "hasUnit" => "uo:Percentage",
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  "rdf:value" => @fastqc_object[:overall_n_content],
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  }
@@ -658,8 +661,8 @@ module Bio
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  def sos_class_for_values
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  [
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  "PhredQualityScore",
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- "NucleotideBaseContent",
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- "SequenceReadContent",
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+ "SequenceBaseAmount",
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+ "SequenceReadAmount",
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  "SequenceReadLength",
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  "SequenceDuplicationLevel",
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  ]
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: bio-fastqc
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  version: !ruby/object:Gem::Version
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- version: 0.6.0
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+ version: 0.7.0
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  platform: ruby
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  authors:
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  - Tazro Inutano Ohta
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2016-04-02 00:00:00.000000000 Z
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+ date: 2016-05-26 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rubyzip