rbbt-sources 3.1.22 → 3.1.23
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/signor.rb +3 -1
- data/lib/rbbt/sources/uniprot.rb +56 -0
- 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: 7e56141cb916b51e2204fac0392eff2d6cd365d1
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data.tar.gz: 9cc540da01980356fdef07b24158f9cc6eb1640b
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: d858ee55af7164f64ae8a4c60519edc242a5f26b08892138df7732c02d0acca887ac4eeda20da62e320718e98dba18457d1be1d821096a66344d33376964486d
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7
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data.tar.gz: c14fb8321b65bfdf1aa93bc490032c84f2d9fb92d98b5d77e816e651fbca4181490292e17e6ba8c6b78c71814707a2aa1a25ff51d97470da5f3fad589386af98
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data/lib/rbbt/sources/signor.rb
CHANGED
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@@ -1,5 +1,6 @@
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require 'rbbt-util'
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require 'rbbt/resource'
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require 'rbbt/sources/uniprot'
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module Signor
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extend Resource
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@@ -63,7 +64,8 @@ module Signor
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require 'rbbt/sources/organism'
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organism = Organism.default_code("Hsa")
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66
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uni2name = Organism.identifiers(organism).index :target => "Associated Gene Name", :fields => ["UniProt/SwissProt Accession"], :persist => true
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#uni2name = Organism.identifiers(organism).index :target => "Associated Gene Name", :fields => ["UniProt/SwissProt Accession"], :persist => true
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uni2name = UniProt.identifiers.Hsa.index :target => "Associated Gene Name", :fields => ["UniProt/SwissProt Accession"], :persist => true
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parser = TSV::Parser.new Signor.data
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fields = parser.fields
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data/lib/rbbt/sources/uniprot.rb
CHANGED
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@@ -9,6 +9,62 @@ module UniProt
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extend Resource
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self.subdir = "share/databases/UniProt"
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def self.get_organism_ids(url, organism = nil)
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tsv = {}
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fields = []
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TSV.traverse url, :type => :array, :bar => "Extracting UniProt IDs #{organism}" do |line|
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uni, type, value = line.split("\t")
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fields << type unless fields.include?(type)
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pos = fields.index type
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values = tsv[uni]
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values = [] if values.nil?
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values[pos] ||= []
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values[pos] << value
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tsv[uni] = values
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end
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fields = fields.collect do |field|
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case field
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when "Gene_Name"
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"Associated Gene Name"
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when "Ensembl"
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"Ensembl Gene ID"
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when "Ensembl_TRS"
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"Ensembl Transcript ID"
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when "Ensembl_PRO"
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"Ensembl Protein ID"
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else
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field
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end
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end
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new = TSV.setup({}, :key_field => "UniProt/SwissProt Accession", :fields => fields, :type => :double, :namespace => organism)
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num_fields = fields.length
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tsv.each do |k,values|
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new_values = [nil] * num_fields
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new_values = values
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num_fields.times do |i|
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new_values[i] = [] if new_values[i].nil?
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end
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new[k] = new_values
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end
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Log.tsv new
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new
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end
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UniProt.claim UniProt.identifiers.Hsa, :proc do
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url = "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz"
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tsv = UniProt.get_organism_ids(url, "Hsa")
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tsv.to_s
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end
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UniProt.claim UniProt.identifiers.Mmu, :proc do
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url = "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/MOUSE_10090_idmapping.dat.gz"
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tsv = UniProt.get_organism_ids(url, "Mmu")
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tsv.to_a
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end
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UniProt.claim UniProt.annotated_variants, :proc do
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url = "http://www.uniprot.org/docs/humsavar.txt"
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tsv = TSV.open(CMD.cmd('tail -n +31 | head -n -4|grep "[[:alpha:]]"', :in => Open.open(url), :pipe => true),
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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: 3.1.
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version: 3.1.23
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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: 2017-12-
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date: 2017-12-07 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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