rbbt-util 5.17.14 → 5.17.15

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 0a87e53388037ba0b25c201b000724d2bd563ae5
+  metadata.gz: c2f8120450462e267978ac9286e307bd6d29479c
+  data.tar.gz: a69e4f7c3487a7f66c45da5d7373b3bc082247c2
 SHA512:
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+  metadata.gz: b4674ad60cab9dd516b0f11de1487e1bbcf59b5136ffe208b238d2c05722c8a522d5048e9983e59af3083a9c7ca3d766c25dac3f13edbe55c4b00a320294b50f
+  data.tar.gz: 54f233ae85fbc65cecb5f541951c894ae85b8190aec13cd808696df9675e2a3041fe59d7929c1d487603fdbae7ac130259c437a711b543c752537257b889eb36

data/lib/rbbt/workflow/accessor.rb

@@ -230,7 +230,8 @@ class Step
   end
 
   def progress_bar(msg, options = {})
-    Log::ProgressBar.new nil, {:desc => msg, :file => file(:progress)}.merge(options)
+    max = options[:max]
+    Log::ProgressBar.new max, {:desc => msg, :file => file(:progress)}.merge(options)
   end
 
   def self.log(status, message, path, &block)
@@ -414,6 +415,7 @@ module Workflow
              end
 
 
+    iii inputs
     dependencies = task_dependencies[name].select{|dep| String === dep or Symbol === dep}
     { :id => File.join(self.to_s, name.to_s),
       :description => description,
@@ -430,7 +432,8 @@ module Workflow
   end
 
   def rec_dependencies(taskname)
-    @rec_dependencies ||= begin
+    @rec_dependencies ||= {}
+    @rec_dependencies[taskname] ||= begin
                             if task_dependencies.include? taskname
                               deps = task_dependencies[taskname]
                               all_deps = deps.select{|dep| String === dep or Symbol === dep or Array === dep}
@@ -470,13 +473,15 @@ module Workflow
     task
   end
 
-  def rec_inputs(taskname)
-    [taskname].concat(rec_dependencies(taskname)).inject([]){|acc, tn| acc.concat(task_from_dep(tn).inputs) }.uniq
-  end
+  #def rec_inputs(taskname)
+  #  [taskname].concat(rec_dependencies(taskname)).inject([]){|acc, tn| acc.concat(task_from_dep(tn).inputs) }.uniq
+  #end
 
   def rec_inputs(taskname)
     task = task_from_dep(taskname)
+    iii rec_dependencies(taskname)
     dep_inputs = task.dep_inputs rec_dependencies(taskname), self
+    iii dep_inputs
     task.inputs + dep_inputs.values.flatten
   end
 

data/share/rbbt_commands/study/maf2study

@@ -0,0 +1,58 @@
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+
+Convert MAF file to Rbbt study
+
+$ rbbt study maf2study [options] <filename.maf> <directory>
+
+-h--help Print this help
+-o--organism* Organism code 
+-w--watson Mutations reported in Watson strand
+
+EOF
+rbbt_usage and exit 0 if options[:help]
+
+raise ParameterException, "Need MAF file and directory" unless ARGV.length == 2
+
+file, directory = ARGV
+
+
+fields = ['Chrom', 'Start_Position', 'Reference_Allele', 'Tumor_Seq_Allele2','Tumor_Sample_Barcode']
+all_fields = TSV.parse_header(file, :header_hash => '').all_fields
+field_pos = fields.collect{|f| all_fields.index f}
+
+sample_mutations = {}
+first = true
+TSV.traverse file, :header_hash => '', :type => :array do |line|
+  if first
+    first = false
+    next
+  end
+  chr, pos, ref, mut, sample = line.split("\t").values_at *field_pos
+  pos, muts = Misc.correct_icgc_mutation(pos, ref, mut)
+  muts.each do |mut|
+    mut = [chr, pos, mut] * ":"
+    sample = sample.split("-").values_at(0,1,2) * "-" if sample =~ /TCGA/
+      sample_mutations[sample] ||= []
+    sample_mutations[sample] << mut
+  end
+end
+
+genotype_dir = File.join(directory, 'genotypes')
+FileUtils.mkdir_p genotype_dir
+
+sample_mutations.each do |sample, mutations|
+  Open.write(File.join(genotype_dir, sample), mutations * "\n")
+end
+
+
+metadata_yaml = File.join(directory, 'metadata.yaml')
+
+metadata = {:organism => "Hsa/feb2014", :watson => "true"}.merge options
+Open.write(metadata_yaml, metadata.to_yaml)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.14
+  version: 5.17.15
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-04-08 00:00:00.000000000 Z
+date: 2015-04-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -301,6 +301,7 @@ files:
 - share/rbbt_commands/stat/abs
 - share/rbbt_commands/stat/density
 - share/rbbt_commands/stat/log
+- share/rbbt_commands/study/maf2study
 - share/rbbt_commands/study/task
 - share/rbbt_commands/system/clean
 - share/rbbt_commands/system/deleted_files
@@ -431,7 +432,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.6
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)