rbbt-sources 3.0.26 → 3.0.27
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/lib/rbbt/sources/corum.rb +45 -0
- metadata +3 -2
checksums.yaml
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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: 181746bb32b62916dc308c6a3de563e9a4cabc38
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data.tar.gz: 83716370f3b9b4b67001c027b2e92376d10e0470
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SHA512:
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metadata.gz:
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metadata.gz: 0e48df6950c1ec5920d90d9572e6afc3077922e78f0df2a8f8a0e9ae239d09ed4eeb6d9b95bc36628e64233d2f5f13a39dbd439d103eda11a0d762b222c38456
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data.tar.gz: 397844dfcd4b57939300c19e88de625291fb083dd1e380145f1edddfb30cbaca54c43d49bbb5981c92c8c47b257e0afc178204ba0e7ea34bba42777dec79b09d
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@@ -0,0 +1,45 @@
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require 'rbbt-util'
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require 'rbbt/resource'
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module CORUM
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extend Resource
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self.subdir = 'share/databases/CORUM'
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def self.organism(org="Hsa")
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Organism.default_code(org)
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end
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CORUM.claim CORUM.complex_names, :proc do
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url = "http://mips.helmholtz-muenchen.de/genre/proj/corum/allComplexes.csv"
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tsv = TSV.open(url, :header_hash => "", :sep => ';', :sep2 => ',', :fix => Proc.new{|l| "CORUM:" + l.gsub('"','')})
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tsv.namespace = organism
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tsv.fields = tsv.fields.collect{|f| f.gsub('"','')}
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tsv.key_field = "CORUM Complex ID"
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tsv.slice("Complex name").to_single
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end
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CORUM.claim CORUM.complexes, :proc do
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url = "http://mips.helmholtz-muenchen.de/genre/proj/corum/allComplexes.csv"
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tsv = TSV.open(url, :header_hash => "", :sep => ';', :sep2 => ',', :fix => Proc.new{|l| "CORUM:" + l.gsub('"','')})
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tsv.namespace = organism
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tsv.fields = tsv.fields.collect{|f| f.gsub('"','')}
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tsv.key_field = "CORUM Complex ID"
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tsv.identifiers = CORUM.complex_names.produce.find
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tsv
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end
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end
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if defined? Entity
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module CORUMComplex
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extend Entity
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self.annotation :format
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self.annotation :organism
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self.add_identifiers CORUM.complex_names, "CORUM Complex ID", "Complex name"
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property :genes => :array2single do
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@genes ||= CORUM.complexes.tsv(:persist => true, :fields => ["subunits (UniProt IDs)"], :type => :flat).values_at *self
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end
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end
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end
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metadata
CHANGED
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@@ -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: 3.0.
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version: 3.0.27
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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: 2015-
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date: 2015-06-08 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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@@ -99,6 +99,7 @@ files:
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- lib/rbbt/sources/bibtex.rb
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- lib/rbbt/sources/biomart.rb
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- lib/rbbt/sources/cath.rb
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- lib/rbbt/sources/corum.rb
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- lib/rbbt/sources/ensembl.rb
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- lib/rbbt/sources/ensembl_ftp.rb
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- lib/rbbt/sources/entrez.rb
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