rbbt-sources 3.1.45 → 3.1.46
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- checksums.yaml +4 -4
- data/lib/rbbt/sources/tfacts.rb +14 -14
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA256:
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-
metadata.gz:
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4
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data.tar.gz:
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3
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metadata.gz: 9cfdfc8f6fd6a11106d90cf39dc8f10165fd36128fe69a8ca4c72fcf878183c3
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4
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data.tar.gz: f268c37d7c50b74fb67d2dae77bf25c93dbf1013f23a11e1ffeb0f024fdabdc0
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SHA512:
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metadata.gz:
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7
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data.tar.gz:
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6
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metadata.gz: d6e29cb4355ad3307bf3ccbead098406e51216e963cd201fc11c17aa4aad263d184ca1ab1389c4940e32bf1d541471a9aac326b12055585b515f26c63592a025
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7
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data.tar.gz: 4663061a1b3f8a80914468c8af3bb8b5da821739fe8943011881ba9b89405e34b40ec9b145e9a7f9fdf7b2cc7cdf8f294fa978b01c41b1f8693a4e73b186d65f
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data/lib/rbbt/sources/tfacts.rb
CHANGED
@@ -2,15 +2,15 @@ require 'rbbt'
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require 'rbbt/tsv'
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require 'rbbt/resource'
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-
module
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5
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+
module TFactS
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extend Resource
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-
self.subdir = "share/databases/
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7
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+
self.subdir = "share/databases/TFactS"
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9
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-
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9
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TFactS.claim TFactS[".source"]["Catalogues.xls"], :url, "http://www.tfacts.org/TFactS-new/TFactS-v2/tfacts/data/Catalogues.xls"
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11
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-
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11
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+
TFactS.claim TFactS.targets, :proc do
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require 'spreadsheet'
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-
book = Spreadsheet.open
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book = Spreadsheet.open TFactS[".source"]["Catalogues.xls"].produce.find
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sheet = book.worksheet 0
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tsv = TSV.setup({}, :key_field => "Target Gene (Associated Gene Name)", :fields => ["Transcription Factor (Associated Gene Name)"], :namespace => "Hsa", :type => :flat)
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@@ -24,9 +24,9 @@ module TFacts
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tsv.to_s
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end
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-
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+
TFactS.claim TFactS.targets_signed, :proc do
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require 'spreadsheet'
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-
book = Spreadsheet.open
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+
book = Spreadsheet.open TFactS[".source"]["Catalogues.xls"].produce.find
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sheet = book.worksheet 1
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tsv = TSV.setup({}, :key_field => "Target Gene (Associated Gene Name)", :fields => ["Transcription Factor (Associated Gene Name)", "Sign", "PMID"], :namespace => "Hsa", :type => :double)
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@@ -43,13 +43,13 @@ module TFacts
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tsv.to_s
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end
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-
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-
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46
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TFactS.claim TFactS.regulators, :proc do
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TFactS.targets.tsv.reorder("Transcription Factor (Associated Gene Name)").to_s
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end
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-
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TFactS.claim TFactS.tf_tg, :proc do
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require 'spreadsheet'
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book = Spreadsheet.open
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book = Spreadsheet.open TFactS[".source"]["Catalogues.xls"].produce.find
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tsv = TSV.setup({}, :key_field => "Transcription Factor (Associated Gene Name)", :fields => ["Target Gene (Associated Gene Name)", "Sign", "Species", "Source", "PMID"], :namespace => "Hsa", :type => :double)
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@@ -128,16 +128,16 @@ if defined? Entity and defined? Gene and Entity === Gene
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module Gene
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property :is_transcription_factor? => :array2single do
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-
tfs =
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tfs = TFactS.targets.keys
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self.name.collect{|gene| tfs.include? gene}
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end
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property :transcription_regulators => :array2single do
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Gene.setup(
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+
Gene.setup(TFactS.regulators.tsv(:persist => true).values_at(*self.name), "Associated Gene Name", self.organism)
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end
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property :transcription_targets => :array2single do
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Gene.setup(
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Gene.setup(TFactS.targets.tsv(:persist => true).values_at(*self.name), "Associated Gene Name", self.organism)
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end
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end
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end
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metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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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.
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+
version: 3.1.46
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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: 2020-
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+
date: 2020-05-14 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
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