rbbt-sources 3.0.30 → 3.0.31

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 3770be50c944954cd02c46a5a28d7c0502810b6b
-  data.tar.gz: b9fce35ae48f309058f314f77e72ca0685262542
+  metadata.gz: bcfbf7826895a76991509420782984e70d8385fe
+  data.tar.gz: 48624bc5d1a71539a4006470229df78631499f2d
 SHA512:
-  metadata.gz: ceb660cc457717662da4ffc3b56159f98f5699e11c59d3ea8f896e03c3b8bb670e7085e953b1088497818255253a7543ef448863219562296391ff3a4d59170f
-  data.tar.gz: b9c443b486bd3b06523b1e2b520c1acbcced1c7d3aa1c1d582df4244cc6a1a95e313588db2809f829677bb41bb1b0bdf8b861ea5d6e6ef08e6bc5fd81ef05c88
+  metadata.gz: eec55666221f0aa738a831b19b6371887bd981565ff0e4b3d4056ab90b2b1f2874b2375379c272d2177e0af8172aba58441f682c78a5c6aa78567f2eb332e7da
+  data.tar.gz: 8b35c2fce2244f219512cc01b1e6d9ce2d2fd598c87c3bbc307fee443cb3ef5c54b9d751b7b22d914ab174e8aa387c3cbd5e69b969e2c5e53b61e31cc1ed0ae3

data/lib/rbbt/sources/clinvar.rb

@@ -0,0 +1,78 @@
+require 'rbbt-util'
+require 'rbbt/resource'
+
+module ClinVar
+  extend Resource
+  self.subdir = 'share/databases/ClinVar'
+
+  def self.organism(org="Hsa")
+    Organism.default_code(org)
+  end
+
+  ClinVar.claim ClinVar.variant_summary, :url, "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz"
+
+  ClinVar.claim ClinVar.snv_summary, :proc do
+    url = "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz"
+    io = TSV.traverse ClinVar.variant_summary, :type => :array, :into => :stream do |line|
+      line = Misc.fixutf8 line
+      begin
+        res = []
+        if line =~ /^#/
+          parts = line.split("\t")
+          res << (["#Genomic Mutation"] + parts[1..12] + parts[15..23]) * "\t"
+        else
+          next unless line =~ /GRCh37/ 
+          next if line =~ /(copy number|NT expansion|duplication|indel)/
+          parts = line.split("\t")
+          chr,pos,ref,mut = parts.values_at 13, 14, 25, 26
+          next if ref == 'na' or mut == 'na'
+
+          pos, muts = Misc.correct_mutation(pos.to_i,ref,mut)
+          muts.each do |mut|
+            mutation = [chr,pos,mut] * ":"
+            res << ([mutation] + parts[1..12] + parts[15..23]) * "\t"
+          end
+        end
+        res.extend MultipleResult
+        res
+      rescue
+        Log.exception $!
+        raise $!
+      end
+    end
+    Misc.sort_stream(io)
+  end
+
+  ClinVar.claim ClinVar.mi_summary, :proc do
+    require 'rbbt/workflow'
+    Workflow.require_workflow "Sequence"
+    variants = ClinVar.snv_summary.produce
+    muts = CMD.cmd('cut -f 1', :in => variants.open, :pipe => true)
+    consequence = Sequence.job(:mutated_isoforms_fast, "Clinvar", :mutations => muts, :non_synonymous => true).clean.run(true)
+
+    options = TSV.parse_header(variants).options.merge({:key_field => "Mutated Isoform"})
+    fields = options[:fields].length
+    dumper = TSV::Dumper.new options
+    dumper.init
+    pasted = TSV.paste_streams([variants, TSV.get_stream(consequence)])
+    TSV.traverse pasted, :into => dumper, :bar => true do |mutation,values|
+      begin
+        mis = values[fields..-1].flatten
+        next if mis.empty?
+        res = []
+        res.extend MultipleResult
+        mis.each do |mi|
+          res << [mi, values[0..fields-1]]
+        end
+        res
+      rescue
+        Log.exception $!
+        raise $!
+      end
+    end
+    dumper.stream
+  end
+end
+
+iif ClinVar.mi_summary.produce(true).find if __FILE__ == $0
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.0.30
+  version: 3.0.31
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-06-24 00:00:00.000000000 Z
+date: 2015-07-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -99,6 +99,7 @@ files:
 - lib/rbbt/sources/bibtex.rb
 - lib/rbbt/sources/biomart.rb
 - lib/rbbt/sources/cath.rb
+- lib/rbbt/sources/clinvar.rb
 - lib/rbbt/sources/corum.rb
 - lib/rbbt/sources/ensembl.rb
 - lib/rbbt/sources/ensembl_ftp.rb