rbbt-sources 3.1.46 → 3.1.47

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 9cfdfc8f6fd6a11106d90cf39dc8f10165fd36128fe69a8ca4c72fcf878183c3
-  data.tar.gz: f268c37d7c50b74fb67d2dae77bf25c93dbf1013f23a11e1ffeb0f024fdabdc0
+  metadata.gz: 6cecde427390fc444e5ef5b6bef42072bf87714b404647c6c086da92a1eaa13a
+  data.tar.gz: 673429c8eab433ec9854c81d52450f8885c57e4b3f8b6779ded44585e6f88343
 SHA512:
-  metadata.gz: d6e29cb4355ad3307bf3ccbead098406e51216e963cd201fc11c17aa4aad263d184ca1ab1389c4940e32bf1d541471a9aac326b12055585b515f26c63592a025
-  data.tar.gz: 4663061a1b3f8a80914468c8af3bb8b5da821739fe8943011881ba9b89405e34b40ec9b145e9a7f9fdf7b2cc7cdf8f294fa978b01c41b1f8693a4e73b186d65f
+  metadata.gz: e39a3a6418bfb514ec786da0128f6fb8437da9728224dacd41b837300680c6d34e821f08954820cb5b7fd064546fee21fd0557d179c469eda969485ffd5cd965
+  data.tar.gz: 9f332f35fcd9c66db7506875efcc7c5276b1f588dd3b70ca299aaa2a7f25c33a650e496ba207af4e12e3bb2a6dfbc9ec8b1f0729e3acedc354145572dd268836

data/etc/biomart/missing_in_archive

@@ -1,3 +1,7 @@
+">oct2014":
+    - rgd~rgd_id
+">jun2019":
+    - entrezgene~entrezgene_id
 ">dec2017":
     - unigene
 ">dec2016":

data/lib/rbbt/sources/biomart.rb

@@ -134,11 +134,14 @@ module BioMart
   # cause an error if the BioMart WS does not allow filtering with that
   # attribute.
   def self.query(database, main, attrs = nil, filters = nil, data = nil, open_options = {})
+    IndiferentHash.setup(open_options)
     open_options = Misc.add_defaults open_options, :nocache => false, :filename => nil, :field_names => nil, :by_chr => false
     filename, field_names, by_chr = Misc.process_options open_options, :filename, :field_names, :by_chr
     attrs   ||= []
     open_options = Misc.add_defaults open_options, :keep_empty => false, :merge => true
 
+    IndiferentHash.setup(open_options)
+
     Log.low "BioMart query: '#{main}' [#{(attrs || []) * ', '}] [#{(filters || []) * ', '}] #{open_options.inspect}"
 
     max_items = 2
@@ -167,6 +170,7 @@ module BioMart
     end
 
     open_options[:filename] = "BioMart[#{main}+#{attrs.length}]"
+
     if filename.nil?
       results = TSV.open data, open_options
       results.key_field = main
@@ -200,6 +204,7 @@ module BioMart
         missing+=v if Organism.compare_archives(current_archive, t) == -1
       elsif k=~ /^>(.*)/ 
         t = $1.strip
+        iii [current_archive, t, Organism.compare_archives(current_archive, t)]
         missing+=v if Organism.compare_archives(current_archive, t) == 1
       end
     end

data/share/install/Organism/Hsa/Rakefile

@@ -5,7 +5,7 @@ require File.join(File.dirname(__FILE__), '../../lib/helpers')
 
 $taxs = [9606]
 $scientific_name = "Homo sapiens"
-$ortholog_key = "human_ensembl_gene"
+$ortholog_key = "hsapiens_homolog_ensembl_gene"
 
 $biomart_db = 'hsapiens_gene_ensembl'
 $biomart_db_germline_variation = 'hsapiens_snp'

data/share/install/Organism/Mmu/Rakefile

@@ -5,7 +5,7 @@ require File.join(File.dirname(__FILE__), '../../lib/helpers')
 
 $taxs = [10090]
 $scientific_name = "Mus musculus"
-$ortholog_key = "mouse_ensembl_gene"
+$ortholog_key = "mmusculus_homolog_ensembl_gene"
 
 $biomart_db = 'mmusculus_gene_ensembl'
 $biomart_db_germline_variation = 'mmusculus_snp'

data/share/install/Organism/Rno/Rakefile

@@ -9,7 +9,7 @@ $scientific_name = "Rattus norvegicus"
 $biomart_db = 'rnorvegicus_gene_ensembl'
 $biomart_db_germline_variation = 'rnorvegicus_snp'
 $biomart_db_somatic_variation = 'rnorvegicus_snp_som'
-$ortholog_key = "rat_ensembl_gene"
+$ortholog_key = "rnorvegicus_homolog_ensembl_gene"
 
 $biomart_lexicon = [ 
   [ 'Associated Gene Name' , "external_gene_id"], 

data/share/install/Organism/organism_helpers.rb

@@ -547,13 +547,13 @@ end
 rule /^possible_ortholog_(.*)/ do |t|
   other = t.name.match(/ortholog_(.*)/)[1]
   other_key = Organism.ortholog_key(other).produce.read
-  BioMart.tsv($biomart_db, $biomart_ensembl_gene, [["Ortholog Ensembl Gene ID", "inter_paralog_" + other_key]], [], nil, :keep_empty => false, :type => :flat, :filename => t.name, :namespace => Thread.current['namespace'])
+  BioMart.tsv($biomart_db, $biomart_ensembl_gene, [["Ortholog Ensembl Gene ID", "inter_paralog_" + other_key]], [], nil, :keep_empty => false, :type => :double, :filename => t.name, :namespace => Thread.current['namespace'])
 end
 
 rule /^ortholog_(.*)/ do |t|
   other = t.name.match(/ortholog_(.*)/)[1]
   other_key = Organism.ortholog_key(other).produce.read
-  BioMart.tsv($biomart_db, $biomart_ensembl_gene, [["Ortholog Ensembl Gene ID", other_key]], [], nil, :keep_empty => false, :type => :flat, :filename => t.name, :namespace => Thread.current['namespace'])
+  BioMart.tsv($biomart_db, $biomart_ensembl_gene, [["Ortholog Ensembl Gene ID", other_key]], [], nil, :keep_empty => false, :type => :double, :filename => t.name, :namespace => Thread.current['namespace'])
 end
 
 rule /[a-z]{3}[0-9]{4}\/.*/i do |t|

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.1.46
+  version: 3.1.47
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-05-14 00:00:00.000000000 Z
+date: 2020-07-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util