cheripic 1.2.6 → 1.2.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: 4b848b1b52f01215fabf404f7387e6f621a2285b
-  data.tar.gz: e434cbad53ac982974c30cf2a940668862a6d2bd
+SHA256:
+  metadata.gz: f24f55bc589e3b5d791c6c19fe7c221df301ba0bc6fbf9026c942a694a2e6941
+  data.tar.gz: f5c70c5e67b23d36267380f39e8c217d8c2635c825234dc23ba423e657f78d4f
 SHA512:
-  metadata.gz: ef7eb0c0008b8d8ed45d6e1deeeb4c59ef187a8af3a92fbc91dba33d91af03b475c337c2e69dcdcb8c34c3cfeea3f9f5d54e42fadba8d0270e0a776c96609c79
-  data.tar.gz: beb3fccf28f54a30fc355a93261043d27dfd4d2ebb34043245404608d1608d2185aae57b8263192ca5973caf1a99c9b9b1614187e5d253656efc9ec9fab9aa50
+  metadata.gz: debd30f6e790b0ba0c4defadd6cd507ea982253e574817afd8af1e83cdcff24e70756a7f548bc37d40c62bf6e1ff25d622c121a55614900e84f9c61a2d8eba69
+  data.tar.gz: 503fb4e4b5a7ce63cac2ea2a739fb622573ef9c20bb9acb1868ab202901f5cde9594ba998b06ff84ec4d06c46954c1e567c636f3f18893a9b4a49a6b605f27a0

data/Rakefile

@@ -64,6 +64,7 @@ def create_package(target)
   sh "mkdir -p #{package_dir}/lib/app/bin"
   sh "cp bin/cheripic #{package_dir}/lib/app/bin/"
   sh "cp -R lib #{package_dir}/lib/app/"
+  sh "unzip test/data/test_data.zip -d #{package_dir}/"
   sh "mkdir #{package_dir}/lib/app/ruby"
   sh "tar -xzf packaging/traveling-ruby-#{TRAVELING_RUBY_VERSION}-#{target}.tar.gz -C #{package_dir}/lib/app/ruby"
   sh "cp packaging/wrapper.sh #{package_dir}/cheripic"

data/cheripic.gemspec

@@ -25,7 +25,7 @@ Gem::Specification.new do |spec|
   spec.add_dependency 'bio-samtools', '~> 2.4.0'
 
   spec.add_development_dependency 'activesupport', '~> 4.2.6'
-  spec.add_development_dependency 'bundler', '~> 1.7.6'
+  spec.add_development_dependency 'bundler', '>= 1.7.6'
   spec.add_development_dependency 'rake', '~> 10.0'
   spec.add_development_dependency 'minitest'
   spec.add_development_dependency 'minitest-reporters', '>= 1.0.17'

data/lib/cheripic/cmd.rb

@@ -70,10 +70,10 @@ module Cheripic
             :default => 0.5
         opt :htlow, 'lower level for categorizing heterozygosity',
             :type => Float,
-            :default => 0.2
+            :default => 0.25
         opt :hthigh, 'high level for categorizing heterozygosity',
             :type => Float,
-            :default => 0.9
+            :default => 0.75
         opt :mindepth, 'minimum read depth at a position to consider for variant calls',
             :type => Integer,
             :default => 6
@@ -235,22 +235,29 @@ low hme-score or bfr score to list in the final output',
 
     # checks if input files are valid
     def check_input_files(inputfiles)
-      check = 0
       inputfiles.each_key do | type |
         inputfiles[type].flatten!
+        check = 0
         inputfiles[type].each do | symbol |
-          if @options[symbol]
+          if @options[symbol] == nil or @options[symbol] == ''
+            if type == :required
+              raise CheripicArgError.new "Options #{inputfiles}, all must be specified. Try --help for further help."
+            end
+          else
             file = @options[symbol]
-            @options[symbol] = File.expand_path(file)
-            next if type == :optional
-            if type == :required and not File.exist?(file)
-              raise CheripicIOError.new "#{symbol} file, #{file} does not exist: "
-            elsif type == :either and File.exist?(file)
-              check = 1
+            if symbol == :bg_bulk or symbol == :bg_bulk_vcf
+              if file.include? ','
+                @options[symbol] = []
+                file.split(',').each do | infile |
+                  @options[symbol] << File.expand_path(infile)
+                  file_exist?(symbol, infile)
+                end
+              end
+            else
+              @options[symbol] = File.expand_path(file)
+              file_exist?(symbol, file)
             end
-          elsif type == :required
-            raise CheripicArgError.new "Options #{inputfiles}, all must be specified. " +
-                                              'Try --help for further help.'
+            check = 1
           end
         end
         if type == :either and check == 0
@@ -260,6 +267,13 @@ low hme-score or bfr score to list in the final output',
       end
     end
 
+    def file_exist?(symbol, file)
+      # checks if a given file exists
+      unless File.exist?(file)
+        raise CheripicIOError.new "#{symbol} file, #{file} does not exist!"
+      end
+    end
+
     # checks if files with output tag name already exists
     def check_output
       if (@options[:output].split('') & %w{# / : * ? ' < > | & $ ,}).any?

data/lib/cheripic/implementer.rb

@@ -75,7 +75,7 @@ module Cheripic
       end
       # print selected variants that could be potential markers or mutation
       out_file = File.open(@options[pos_type], 'w')
-      out_file.puts "Score\tAlleleFreq\tlength\tseq_id\tposition\tref_base\tcoverage\tbases\tbase_quals\tsequence_left\tAlt_seq\tsequence_right"
+      out_file.puts "HMES\tAlleleFreq\tlength\tseq_id\tposition\tref_base\tcoverage\tbases\tbase_quals\tsequence_left\tAlt_seq\tsequence_right"
       regions = Regions.new(@options.assembly)
       @variants.send(pos_type).each_key do | frag |
         contig_obj = @variants.assembly[frag]

data/lib/cheripic/options.rb

@@ -9,8 +9,8 @@ module Cheripic
     # Default parameter settings
     @def_settings = {
         :hmes_adjust => 0.5,
-        :htlow => 0.2,
-        :hthigh => 0.9,
+        :htlow => 0.25,
+        :hthigh => 0.75,
         :mindepth => 6,
         :maxdepth => 0,
         :max_d_multiple => 5,

data/lib/cheripic/variants.rb

@@ -78,20 +78,29 @@ module Cheripic
       %i{mut_bulk bg_bulk mut_parent bg_parent}.each do | input |
         infile = @params[input]
         if infile != ''
-          logger.info "processing #{input} file"
-          if @params.input_format == 'pileup'
-            extract_pileup(infile, input)
-          elsif @params.input_format == 'vcf'
-            extract_vcfs(infile, input)
+          if infile.kind_of?(Array) and input == :bg_bulk
+            infile.each do | file |
+              send_file_to_extract(file, input)
+            end
           else
-            extract_bam_pileup(infile, input)
+            send_file_to_extract(infile, input)
           end
         end
       end
-
       @pileups_analyzed = true
     end
 
+    def send_file_to_extract(infile, input)
+      logger.info "processing #{input} file"
+      if @params.input_format == 'pileup'
+        extract_pileup(infile, input)
+      elsif @params.input_format == 'vcf'
+        extract_vcfs(infile, input)
+      else
+        extract_bam_pileup(infile, input)
+      end
+    end
+
     # Input vcf file is read and positions are selected that pass the thresholds
     # @param vcffile [String] path to the pileup file to read
     # @param sym [Symbol] Symbol of the pileup file used to write selected variants

data/lib/cheripic/vcf.rb

@@ -68,8 +68,19 @@ module Cheripic
     def self.filtering(mutant_vcf, bgbulk_vcf)
       var_pos_mut = get_vars(mutant_vcf)
       return var_pos_mut if bgbulk_vcf == ''
-      var_pos_bg = get_vars(bgbulk_vcf)
+      if bgbulk_vcf.kind_of?(Array)
+        bgbulk_vcf.each do | file |
+          var_pos_bg = get_vars(file)
+          var_pos_mut = subtract(var_pos_mut,var_pos_bg)
+        end
+      else
+        var_pos_bg = get_vars(bgbulk_vcf)
+        return subtract(var_pos_mut,var_pos_bg)
+      end
+      var_pos_mut
+    end
 
+    def self.subtract(var_pos_mut, var_pos_bg)
       # if both bulks have homozygous mutations at same positions then deleting them
       var_pos_mut.each_key do | frag |
         positions = var_pos_mut[frag][:hom].keys

data/lib/cheripic/version.rb

@@ -2,6 +2,6 @@ module Cheripic
 
   # Sets the semantic version number for this module.
   # Version number will be used in help messages and for generating gem.
-  VERSION = '1.2.6'
+  VERSION = '1.2.7'
 
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: cheripic
 version: !ruby/object:Gem::Version
-  version: 1.2.6
+  version: 1.2.7
 platform: ruby
 authors:
 - Shyam Rallapalli
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2016-10-26 00:00:00.000000000 Z
+date: 2018-07-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: yell
@@ -102,14 +102,14 @@ dependencies:
   name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.7.6
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.7.6
 - !ruby/object:Gem::Dependency
@@ -267,7 +267,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.3
+rubygems_version: 2.7.6
 signing_key: 
 specification_version: 4
 summary: picks causative mutation from bulks segregant sequencing