bio-fastqc 0.10.2 → 0.10.4
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 +5 -5
- data/VERSION +1 -1
- data/lib/bio/fastqc/semantics.rb +39 -36
- data/spec/stdin_fastqc.zip +0 -0
- metadata +4 -3
checksums.yaml
CHANGED
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---
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metadata.gz:
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data.tar.gz:
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SHA256:
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metadata.gz: ee05612afd7abcb08e1a6df37c16e23af1d1dff69212356b8fee08868130db8a
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data.tar.gz: c97b10724023afe960ae41af729276300f103d1ccd6d6bf8f3eac57fc9caf847
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 4e799be0e1a4b502ae58e8e8df109be253aea9d7eac787e7bc73bb0f5db6c1d9ca0738914a88a2abc1b297e1a1046dd807dd70cd70b974555a3c6c57be118702
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data.tar.gz: ca9ce91aca5779567369c21d9c531f157f4c9637af606669595fd308955533b564d7769f0afea24f8eab268d78897f3b27d0f3e82ae437feaef7288b9300d7b2
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data/VERSION
CHANGED
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@@ -1 +1 @@
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1
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-
0.10.
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1
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0.10.4
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data/lib/bio/fastqc/semantics.rb
CHANGED
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@@ -71,7 +71,10 @@ module Bio
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"@type" => "SequenceStatisticsReport",
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"dcterms:identifier" => identifier_literal,
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"dcterms:contributor" => ["Tazro Ohta", "Shuichi Kawashima"],
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"dcterms:created" =>
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"dcterms:created" => {
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"@value" => Time.now.strftime("%Y-%m-%d"),
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"@type" => "xsd:date"
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},
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"dcterms:license" => {
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"@id" => "http://creativecommons.org/licenses/by-sa/4.0/",
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},
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@@ -167,7 +170,7 @@ module Bio
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def total_sequences
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{
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"@type" => "totalSequences",
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"sio:SIO_000221" => "obo:UO_0000244",
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"sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
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"sio:SIO_000300" => {
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"@value" => @fastqc_object[:total_sequences],
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"@type" => "xsd:integer",
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@@ -178,7 +181,7 @@ module Bio
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def filtered_sequences
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{
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"@type" => "filteredSequences",
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"sio:SIO_000221" => "obo:UO_0000244",
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"sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
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"sio:SIO_000300" => {
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"@value" => @fastqc_object[:filtered_sequences],
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"@type" => "xsd:integer",
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def sequence_length
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{
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"@type" => "SequenceReadLength",
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"sio:SIO_000221" => "obo:UO_0000244",
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"sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
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"sio:SIO_000300" => {
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"@value" => @fastqc_object[:sequence_length],
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"@type" => "xsd:string",
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@@ -200,7 +203,7 @@ module Bio
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def percent_gc
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{
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"@type" => "percentGC",
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"sio:SIO_000221" => "obo:UO_0000187",
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"sio:SIO_000221" => { "@id" => "obo:UO_0000187" },
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"sio:SIO_000300" => {
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"@value" => @fastqc_object[:percent_gc],
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"@type" => "xsd:decimal",
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"basePosition" => base,
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"meanBaseCallQuality" => {
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"@type" => "PhredQualityScore",
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"sio:SIO_000221" => "obo:UO_0000189",
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"sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
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"sio:SIO_000300" => mean,
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},
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"medianBaseCallQuality" => {
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"@type" => "PhredQualityScore",
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"sio:SIO_000221" => "obo:UO_0000189",
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"sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
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"sio:SIO_000300" => median,
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},
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"baseCallQualityLowerQuartile" => {
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"@type" => "PhredQualityScore",
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"sio:SIO_000221" => "obo:UO_0000189",
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"sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
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"sio:SIO_000300" => lower_quartile,
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},
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"baseCallQualityUpperQuartile" => {
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"@type" => "PhredQualityScore",
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"sio:SIO_000221" => "obo:UO_0000189",
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"sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
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"sio:SIO_000300" => upper_quartile,
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},
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"baseCallQuality10thPercentile" => {
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"@type" => "PhredQualityScore",
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"sio:SIO_000221" => "obo:UO_0000189",
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"sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
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"sio:SIO_000300" => tenth_percentile,
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},
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"baseCallQuality90thPercentile" => {
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"@type" => "PhredQualityScore",
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"sio:SIO_000221" => "obo:UO_0000189",
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"sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
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"sio:SIO_000300" => ninetieth_percentile,
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},
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}
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"rowIndex" => i,
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"baseCallQuality" => {
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"@type" => "PhredQualityScore",
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"sio:SIO_000221" => "obo:UO_0000189",
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"sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
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"sio:SIO_000300" => quality,
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},
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"sequenceReadCount" => {
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"@type" => "SequenceReadAmount",
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"sio:SIO_000221" => "obo:UO_0000244",
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"sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
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"sio:SIO_000300" => count,
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},
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}
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"basePosition" => base,
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"percentGuanine" => {
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"@type" => "BaseRatio",
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"sio:SIO_000221" => "obo:UO_0000187",
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"sio:SIO_000221" => { "@id" => "obo:UO_0000187" },
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"sio:SIO_000300" => guanine,
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},
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"percentAdenine" => {
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"@type" => "BaseRatio",
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"sio:SIO_000221" => "obo:UO_0000187",
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"sio:SIO_000221" => { "@id" => "obo:UO_0000187" },
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"sio:SIO_000300" => adenine,
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},
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"percentThymine" => {
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"@type" => "BaseRatio",
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"sio:SIO_000221" => "obo:UO_0000187",
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"sio:SIO_000221" => { "@id" => "obo:UO_0000187" },
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"sio:SIO_000300" => thymine,
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},
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"percentCytosine" => {
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"@type" => "BaseRatio",
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"sio:SIO_000221" => "obo:UO_0000187",
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"sio:SIO_000221" => { "@id" => "obo:UO_0000187" },
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"sio:SIO_000300" => chytosine,
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},
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}
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"rowIndex" => i,
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"percentGC" => {
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"@type" => "BaseRatio",
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"sio:SIO_000221" => { "@id" => "obo:UO_0000187" },
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"sio:SIO_000300" => gc_content,
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"sequenceReadCount" => {
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"sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
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"sio:SIO_000300" => count,
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"basePosition" => base,
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"nCount" => {
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"sio:SIO_000221" => { "@id" => "obo:UO_0000187" },
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"sio:SIO_000300" => n_count,
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"sequenceReadLength" => {
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"sio:SIO_000221" => "obo:UO_0000244",
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"sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
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"sio:SIO_000300" => length,
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},
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"sequenceReadCount" => {
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"sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
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}
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"sequenceDuplicationLevel" => {
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"sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
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"sio:SIO_000300" => duplication_level,
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"sequenceReadRelativeCount" => {
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"sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
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"sio:SIO_000300" => relative_count,
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}
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"overrepresentedSequence" => sequence,
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"sequenceReadCount" => {
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"sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
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"sequenceReadPercentage" => {
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"sio:SIO_000221" => { "@id" => "obo:UO_0000187" },
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"sio:SIO_000300" => percentage,
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"possibleSourceOfSequence" => possible_source,
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"kmerSequence" => sequence,
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"observedPerExpectedOverall" => {
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"sio:SIO_000221" => { "@id" => "obo:Ratio" },
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"sio:SIO_000300" => ratio_overall,
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"observedPerExpectedMax" => {
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"observedPerExpectedMaxPosition" => ratio_max_position,
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def min_length
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def max_length
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def mean_sequence_length
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"sio:SIO_000221" => { "@id" => "obo:UO_0000244" },
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def median_sequence_length
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584
|
-
"sio:SIO_000221" => "obo:UO_0000189",
|
|
587
|
+
"sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
|
|
585
588
|
"sio:SIO_000300" => {
|
|
586
589
|
"@value" => @fastqc_object[:overall_mean_quality_score],
|
|
587
590
|
"@type" => "xsd:decimal",
|
|
@@ -592,7 +595,7 @@ module Bio
|
|
|
592
595
|
def overall_median_quality_score
|
|
593
596
|
{
|
|
594
597
|
"@type" => "medianBaseCallQuality",
|
|
595
|
-
"sio:SIO_000221" => "obo:UO_0000189",
|
|
598
|
+
"sio:SIO_000221" => { "@id" => "obo:UO_0000189" },
|
|
596
599
|
"sio:SIO_000300" => {
|
|
597
600
|
"@value" => @fastqc_object[:overall_median_quality_score],
|
|
598
601
|
"@type" => "xsd:decimal",
|
|
@@ -603,7 +606,7 @@ module Bio
|
|
|
603
606
|
def overall_n_content
|
|
604
607
|
{
|
|
605
608
|
"@type" => "nContent",
|
|
606
|
-
"sio:SIO_000221" => "obo:UO_0000187",
|
|
609
|
+
"sio:SIO_000221" => { "@id" => "obo:UO_0000187" },
|
|
607
610
|
"sio:SIO_000300" => {
|
|
608
611
|
"@value" => @fastqc_object[:overall_n_content],
|
|
609
612
|
"@type" => "xsd:decimal",
|
|
Binary file
|
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: bio-fastqc
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.10.
|
|
4
|
+
version: 0.10.4
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Tazro Inutano Ohta
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date:
|
|
11
|
+
date: 2018-07-21 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: rubyzip
|
|
@@ -232,6 +232,7 @@ files:
|
|
|
232
232
|
- spec/example_fastqc.zip
|
|
233
233
|
- spec/example_fastqc_454.zip
|
|
234
234
|
- spec/spec_helper.rb
|
|
235
|
+
- spec/stdin_fastqc.zip
|
|
235
236
|
homepage: http://github.com/inutano/bioruby-fastqc
|
|
236
237
|
licenses:
|
|
237
238
|
- MIT
|
|
@@ -252,7 +253,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
|
252
253
|
version: '0'
|
|
253
254
|
requirements: []
|
|
254
255
|
rubyforge_project:
|
|
255
|
-
rubygems_version: 2.6
|
|
256
|
+
rubygems_version: 2.7.6
|
|
256
257
|
signing_key:
|
|
257
258
|
specification_version: 4
|
|
258
259
|
summary: ruby parser for FastQC output
|