bio-fastqc 0.6.0 → 0.7.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/lib/bio/fastqc/semantics.rb +26 -23
- metadata +2 -2
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: d2d38d1a029d00c2d5d4b986245ae1ed97df914a
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data.tar.gz: c45aecab279bff261d7aeabd8552e9077c97b147
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 0d74e381150aec1772d24fd9178981a6edc6ef59e5c89b5ae9fc3858ebbf64751d8b313a3b36c1563ed1cb4f8df2b076d16e554a653445a70f1ea88398c10200
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7
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data.tar.gz: db39e89d15b366f73e3203cfc130946d0c794aea1e43ee0f7aa68f0af042a2f6fd4262c2a21b740c00277c655567cf31dbdfc106f3dbc17fbfc440768618372b
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data/VERSION
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@@ -1 +1 @@
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1
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0.
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1
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+
0.7.0
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data/lib/bio/fastqc/semantics.rb
CHANGED
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@@ -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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-
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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" => "
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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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}
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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" => "
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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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}
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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" => "
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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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}
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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" => "
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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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@@ -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" => "
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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" => "
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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" => "
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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" => "
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"@type" => "SequenceBaseAmount",
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"hasUnit" => "uo:Percentage",
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"rdf:value" => chytosine,
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},
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"@type" => "Row",
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"rowIndex" => i,
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"percentGC" => {
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"@type" => "
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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" => "
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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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@@ -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" => "SequenceBaseAmount",
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"hasUnit" => "uo:Percentage",
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"rdf:value" => n_count,
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},
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"rdf:value" => length,
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},
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"sequenceReadCount" => {
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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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@@ -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" => "SequenceReadAmount",
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"hasUnit" => "uo:CountUnit",
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"rdf:value" => relative_count,
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},
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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" => "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" => "
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"@type" => "SequenceReadAmount",
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"hasUnit" => "uo:Percentage",
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"rdf:value" => percentage,
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},
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"rowIndex" => i,
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"kmerSequence" => sequence,
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"sequenceReadCount" => {
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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" => "
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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" => "SequenceReadAmount",
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"hasUnit" => "uo:Ratio",
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"rdf:value" => ratio_max,
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},
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def overall_n_content
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{
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"overallNContent" => {
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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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}
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def sos_class_for_values
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[
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"PhredQualityScore",
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"
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"
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"SequenceBaseAmount",
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"SequenceReadAmount",
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"SequenceReadLength",
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"SequenceDuplicationLevel",
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]
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metadata
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1
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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.
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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-
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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
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