rbbt-sources 3.2.14 → 3.2.16

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 476a20bf7be9718acce0355dccc7f88105e168247348de1895491bbf7189b7d2
-  data.tar.gz: a434af060363f85fe565f9f394aa0a64acae7bf58bf98859159536c59be51a11
+  metadata.gz: 0745fa19486f2c9c8c86b24ddf5f44689aa010c500db0bf7fadfc67e03072bf8
+  data.tar.gz: b6d5f1481202d3f191b725f5c0021c371a4f044e14661d3534d31a260ffb480e
 SHA512:
-  metadata.gz: e9f09c7a4514edaf3aabd89a5980d6be18d4761d72676da8be74625617f330b36816f66054fc6af5913ed9d94f6427391dec951307be23a2846225e1c840a813
-  data.tar.gz: 4b07413c9c8e8c6dd64180a1cdbb86407f81b86db8b14c63ff330a17d766b5604014f34dd3346bc6062029dd3c1dd4c1a2bdcaabb3b8cfa96434ba0170da32d6
+  metadata.gz: 1241babce1692c616242e1ef5a501c5e337f3b042110fca932ee3e320ade576538be40723968eabac97ea02133d58144275f5949c3288926d87fc03192417522
+  data.tar.gz: 53b45cbb861f44f2f4f51f4e14a36c3f70210d729f45138228ac06a542857162e94f736b0b43a107af413da0ff68247061e4d99a774932fa5b4f65b3547205c3

data/etc/allowed_biomart_archives

@@ -4,3 +4,4 @@ may2017
 apr2019
 feb2021
 feb2023
+oct2016

data/lib/rbbt/sources/PRO.rb

@@ -14,7 +14,7 @@ module PRO
   #self.search_paths[:default] = :lib
 
   PRO.claim PRO.identifiers, :proc do 
-    url = "ftp://ftp.pir.georgetown.edu/databases/ontology/pro_obo/PRO_mappings/uniprotmapping.txt"
+    url = "ftp://ftp.proteininformationresource.org/databases/ontology/pro_obo/PRO_mappings/uniprotmapping.txt"
 
     dumper = TSV::Dumper.new :key_field => "PRO ID", :fields => ["UniProt/SwissProt Accession"], :type => :double, :namespace => PRO.organism
     dumper.init
@@ -22,7 +22,7 @@ module PRO
       pro, uni = line.split("\t")
       [pro, [uni.split(":").last]]
     end
-    TSV.collapse_stream dumper
+    dumper.tsv merge: true
   end
 
   PRO.claim PRO.uniprot_equivalences, :proc do

data/lib/rbbt/sources/go.rb

@@ -18,7 +18,7 @@ module GO
 
 
   MULTIPLE_VALUE_FIELDS = %w(is_a)
-  TSV_GENE_ONTOLOGY = File.join(Persist.cachedir, 'gene_ontology')
+  #TSV_GENE_ONTOLOGY = File.join(Persist.cachedir, 'gene_ontology')
 
   # This method needs to be called before any translations can be made, it is
   # called automatically the first time the id2name method is called. It loads

data/lib/rbbt/sources/organism.rb

@@ -73,6 +73,7 @@ module Organism
     url = "http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver"
     CMD.cmd_log("wget '#{url}' -O '#{file}'")
     CMD.cmd("chmod 0755 '#{file}'")
+    Rbbt.set_software_env
     nil
   end
 

data/lib/rbbt/sources/signor.rb

@@ -57,7 +57,7 @@ module Signor
     #uni2name = Organism.identifiers(organism).index :target => "Associated Gene Name", :fields => ["UniProt/SwissProt Accession"], :persist => true
     uni2name = UniProt.identifiers.Hsa.index :target => "Associated Gene Name", :fields => ["UniProt/SwissProt Accession"], :persist => true
 
-    parser = TSV::Parser.new Signor.data
+    parser = TSV::Parser.new Signor.data.produce
     fields = parser.fields
     dumper = TSV::Dumper.new :key_field => "Source (UniProt/SwissProt Accession)", :fields => ["Target (Associated Gene Name)", "Effect", "Sign", "PMID"], :type => :double, :merge => true, :organism => Signor.organism
     dumper.init

data/lib/rbbt/sources/tfacts.rb

@@ -114,6 +114,7 @@ module TFactS
         pmids = "" if pmids.nil?
 
         values = [target, "", species, source, pmids]
+        values = values.collect{|v| [v]}
         tsv.zip_new(tf, values)
       end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.2.14
+  version: 3.2.16
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-03-29 00:00:00.000000000 Z
+date: 2023-10-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -24,20 +24,6 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 4.0.0
-- !ruby/object:Gem::Dependency
-  name: nokogiri
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
 - !ruby/object:Gem::Dependency
   name: net-ftp
   requirement: !ruby/object:Gem::Requirement
@@ -178,7 +164,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.26
+rubygems_version: 3.4.19
 signing_key: 
 specification_version: 4
 summary: Data sources for the Ruby Bioinformatics Toolkit (rbbt)