rbbt-sources 3.1.40 → 3.1.41

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 58f9941a36498e575420dbe3fd97c726269e168d4565fa0e587d002706c6f6d6
-  data.tar.gz: 0c684724f4a5d9a4290c4e74f22f3d84dca18c31ec270eed8075649ea8cf6032
+  metadata.gz: e0a35626b221e15867cb54ca9e8bbeb007762b5a99afed75d57d6b473385c287
+  data.tar.gz: 59d067abbfdcd686f39b3604282a280ca9bf4a0e8f3284698202dae8d9d50d55
 SHA512:
-  metadata.gz: e31b8a35bf7cc518cb825003ff6d521c4d94cca64f2adb4f8da7fb634bd9882e135875e1df8ed8d1cacb458e7f1dc9916c1d18281437569c37021ed18d6d38ec
-  data.tar.gz: f942919c06a57079b74414829c0bfcc9c46be2cfc2c8213ed7293d20c00fedad1ec4cc94e4d9b581746f7c0e7430793562e81df5d6a18797aa87e099434a4c27
+  metadata.gz: 1c9c6a2dc5184319e94af671762227bba331b49784cf3e4ac0550b6c023c7b072920d75175b0547c2d8cb4034dbca53dda9514238773cf98f103cc6be978c4ec
+  data.tar.gz: df52691bf65b891a906217f5e2647577bc74940bbd3fa1752115f624a313472a70a43fb96b786e30a4612bc71badb7b3e68c539e0024fe0f0958ee5f33d910af

data/etc/allowed_biomart_archives

@@ -6,3 +6,4 @@ dec2014
 dec2015
 oct2016
 may2017
+apr2019

data/etc/biomart/missing_in_archive

@@ -1,3 +1,5 @@
+">dec2017":
+    - unigene
 ">dec2016":
     - uniprot_swissprot_accession~uniprotswissprot
     - uniprot_swissprot~uniprotswissprot

data/lib/rbbt/sources/signor.rb

@@ -102,7 +102,6 @@ module Signor
   end
 
   Signor.claim Signor.phospho_sites, :proc do
-    uni2name = UniProt.identifiers.Hsa.index :target => "Associated Gene Name", :fields => ["UniProt/SwissProt Accession"], :persist => true
 
     dumper = TSV::Dumper.new :key_field => "Phosphosite", :fields => ["Effect"], :type => :flat, :organism => Signor.organism
     dumper.init
@@ -119,10 +118,8 @@ module Signor
                  else
                    next
                  end
-        name = uni2name[target]
-        next if name.nil?
         next if residue.nil? or residue.empty?
-        site = [name, residue] * ":"
+        site = [target, residue] * ":"
         positive = effect.include? "up-regulates"
 
         activates = kinase && positive || (!kinase && !positive)

data/lib/rbbt/sources/uniprot.rb

@@ -66,7 +66,7 @@ module UniProt
 
 
   UniProt.claim UniProt.annotated_variants, :proc do
-    url = "http://www.uniprot.org/docs/humsavar.txt"
+    url = "https://www.uniprot.org/docs/humsavar.txt"
     tsv = TSV.open(CMD.cmd('tail -n +31 | head -n -4|grep "[[:alpha:]]"', :in => Open.open(url), :pipe => true), 
                    :fix => Proc.new{|line| parts = line.split(/\s+/); (parts[1..5] + [(parts[6..-1] || []) * " "]) * "\t"}, 
                    :type => :double,
@@ -89,8 +89,8 @@ module UniProt
     tsv.to_s
   end
 
-  UNIPROT_TEXT="http://www.uniprot.org/uniprot/[PROTEIN].txt"
-  UNIPROT_FASTA="http://www.uniprot.org/uniprot/[PROTEIN].fasta"
+  UNIPROT_TEXT="https://www.uniprot.org/uniprot/[PROTEIN].txt"
+  UNIPROT_FASTA="https://www.uniprot.org/uniprot/[PROTEIN].fasta"
 
   def self.get_uniprot_entry(uniprotids)
     _array = Array === uniprotids

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.1.40
+  version: 3.1.41
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-07-22 00:00:00.000000000 Z
+date: 2019-11-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -190,7 +190,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
+rubygems_version: 3.0.6
 signing_key: 
 specification_version: 4
 summary: Data sources for the Ruby Bioinformatics Toolkit (rbbt)