rbbt-sources 3.1.39 → 3.1.40

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Files changed (3) hide show
  1. checksums.yaml +4 -4
  2. data/lib/rbbt/sources/CASCADE.rb +9 -3
  3. metadata +2 -2
checksums.yaml CHANGED
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+ data.tar.gz: f942919c06a57079b74414829c0bfcc9c46be2cfc2c8213ed7293d20c00fedad1ec4cc94e4d9b581746f7c0e7430793562e81df5d6a18797aa87e099434a4c27
@@ -39,16 +39,23 @@ module CASCADE
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  associations = {}
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  interactions.through do |source, values|
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- values.zip_fields.each do |target,typea,ida,databasea,typeb,idb,databaseb,effect|
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+ Misc.zip_fields(values.values_at("ENTITYB", "TYPEA", "IDA","DATABASEA", "TYPEB", "IDB", "DATABASEB", "EFFECT")).each do |target,typea,ida,databasea,typeb,idb,databaseb,effect|
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  next if typea == 'gene'
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+ typea.strip!
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+ typeb.strip!
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+
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+ typea = 'output' if typea == 'phenotype'
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+ typeb = 'output' if typeb == 'phenotype'
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  if typeb == 'gene'
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  target.sub!('_g','')
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  type = '-t'
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  elsif typeb == 'output' or typea == 'output'
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  type = '-ap'
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- else
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+ elsif typeb == 'protein' or typeb == 'protein family' or typeb == 'protein complex' or typeb == 'second messenger'
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  type = '-a'
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+ else
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+ raise "Unknown type #{typeb} #{source} #{target}"
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  end
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  proteins << source unless source.include? '_f' or source.include? '_c'
@@ -93,7 +100,6 @@ module CASCADE
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  end
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  end
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-
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  associations.each do |p,i|
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  source, target = p
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  type, symbol = i
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: rbbt-sources
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  version: !ruby/object:Gem::Version
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- version: 3.1.39
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+ version: 3.1.40
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  platform: ruby
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  authors:
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  - Miguel Vazquez
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2019-07-05 00:00:00.000000000 Z
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+ date: 2019-07-22 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rbbt-util