rbbt-util 5.19.7 → 5.19.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 32e7e5890ca727590d4b83985dd6812298d9312d
-  data.tar.gz: 05af8d4902b8e1b6438c369c5e53500152d32705
+  metadata.gz: 70a20a4985413f36348028410a914cb78fbf4795
+  data.tar.gz: 52aef24051104d8a63c3c84839abb479964d1b08
 SHA512:
-  metadata.gz: 58b0b9a4d3a7199b4a2973358c35b8fabf3bd7fbe38d4bf9bd5faa638ab6f72ff4b54d592ee90cc80cd1b2d2f85c29f307c521715af30aadb7fadff18dc4948f
-  data.tar.gz: 2f36800fbf43fc479546b09a28f4d59ae5c88c7222c489efc37907a17fedfaabcaba74144f70e3939b7f14be58d75602354e539bfc7af07a84ecdf3cd27e3d19
+  metadata.gz: 7b45d1c76971f7450d105ac1a817f0bcc87d3dbbec0427de52921844b8ea485bda96c2eed28f3bcebb056e57165c3f66cdb6577ec8f9bd4d8e9944d0a6dd9100
+  data.tar.gz: 60203a5f62caf8993bb33e58e4720efa941307b791d1ca6be05cf67a63913d2f27e27d7ff1a584e2d60b288565151b8c2568325636cef551a289d77501cdb47f

data/etc/app.d/finder.rb

@@ -17,6 +17,9 @@ if ENV['RBBT_FINDER']
 
   organism_hash = {"organism" => /[A-Z][a-z]{2}(?:\/[a-z]{3}20\d\d)?/}
   finder.add_instance(organism_hash, :namespace => organism) 
+
+  snp_hash = {"SNP" => /^rs\d+$/}
+  finder.add_instance(snp_hash, :namespace => organism) 
 end
 set :finder, finder
 Log.debug("Finder started with: #{finder.instances.length} instances")

data/lib/rbbt/util/R/plot.rb

@@ -19,6 +19,7 @@ module R
         end
         values = [values] unless Array === values
         field_classes = values.collect do |v| 
+          v = v.first if Array === v
           case v
           when FalseClass, TrueClass
             "'logical'"

data/share/rbbt_commands/tsv/attach

@@ -14,6 +14,7 @@ $ rbbt tsv attach <file1> <file2> [<file3> ...] [options]
 Use - to read from STDIN
 
 -f--fields* Fields to attach (all if not specified)
+-i--identifiers* Identifier file
 -h--help Print this help
 
 EOF
@@ -28,15 +29,21 @@ end
 
 file1, *rest = ARGV
 fields = options[:fields]
+identifiers = options[:identifiers] 
+
+if identifiers.nil?
+  require 'rbbt/sources/organism'
+  Organism.identifiers(Organism.default_code("Hsa"))
+end
 
 fields = fields ? fields.split(/[,|]/).collect{|f| f.strip} : nil
 
-tsv = TSV.open(file1)
+tsv = TSV.open(file1, :unnamed => true)
 
 rest.each do |file2|
   file_fields = TSV.parse_header(file2).all_fields - tsv.all_fields
   these_fields = fields ? fields & file_fields : nil
-  tsv = tsv.attach file2, :fields => these_fields
+  tsv = tsv.attach file2, :fields => these_fields, :identifiers => identifiers
 end
 
 puts tsv.to_s

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.19.7
+  version: 5.19.8
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-11-27 00:00:00.000000000 Z
+date: 2015-12-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake