rbbt-util 5.21.130 → 5.21.131

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: cae5ae771a6fb59164c08952b189d399343e2be7
+  metadata.gz: 30f68eea441653388fb59fd05ae206e5b120b8eb
+  data.tar.gz: 88a93f9598386c6605e086ce575c2d0ff31a3146
 SHA512:
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-  data.tar.gz: b4aaa61f8fe810af9f0a6bdcf45b95bd6903563ffe21421f7987a7701f03af6c3fcb2dcb8be5c62ebc6ea842502229f9577bb2c2f5dbf87f01818fbb71854b21
+  metadata.gz: 2d21f9912e46073ec0c7593e15702be44445f9928405d70a5dd9c2d92c53d42cd0f04be8c9a33f9dd6dd29229ca4ec39a902cf3dc55682b15b7c9c081a5092c0
+  data.tar.gz: 22a459d7ed570054f06d3d33b9202ac577bded51a21c105669afa7e1d3cff160973a9f03bf3252f88518ade85418ba087430426f9fc5ecb3f3b7bcbdc9539c26

data/lib/rbbt/tsv/accessor.rb

@@ -574,7 +574,20 @@ module TSV
         if keys
           keys.each do |key|
             if unmerge
-              Misc.zip_fields(self[key]).each do |values|
+              value_list = self[key]
+              max = value_list.collect{|v| v.length}.max
+
+              if unmerge == :expand and max > 1
+                value_list = value_list.collect do |values|
+                  if values.length == 1
+                    [values.first] * max
+                  else
+                    values
+                  end
+                end
+              end
+              
+              Misc.zip_fields(value_list).each do |values|
                 dumper.add key, values
               end
             else
@@ -583,14 +596,26 @@ module TSV
           end
         else
           with_unnamed do
-            each do |k,v|
+            each do |k,value_list|
 
               if unmerge
-                Misc.zip_fields(v).each do |values|
+                max = value_list.collect{|v| v.length}.max
+
+                if unmerge == :expand and max > 1
+                  value_list = value_list.collect do |values|
+                    if values.length == 1
+                      [values.first] * max
+                    else
+                      values
+                    end
+                  end
+                end
+
+                Misc.zip_fields(value_list).each do |values|
                   dumper.add k, values
                 end
               else
-                dumper.add k, v
+                dumper.add k, value_list
               end
             end
           end
@@ -625,6 +650,14 @@ module TSV
     str
   end
 
+  def to_unmerged_s(keys = nil, no_options = false)
+    to_s keys, no_options, true
+  end
+
+  def to_unmerged_expanded_s(keys = nil, no_options = false)
+    to_s keys, no_options, :expand
+  end
+
   def value_peek
     peek = {}
     i = 0

data/lib/rbbt/tsv/excel.rb

@@ -100,9 +100,18 @@ module TSV
       text = Misc.process_options options, :text
 
       header = true unless header == false
-      sheet ||= 0
-      TmpFile.with_file do |filename|
-        workbook = Spreadsheet.open Open.open(file)
+      sheet ||= "0"
+
+      workbook = Spreadsheet.open Open.open(file)
+
+      if sheet && sheet.to_s =~ /^\d+$/
+        sheet = workbook.worksheets.collect{|s| s.sheet_name }[sheet.to_i]
+      end
+      sheet_name = sheet
+      Log.debug "Opening LSX #{file} sheet #{ sheet_name }"
+
+      TmpFile.with_file :extension => Misc.sanitize_filename(sheet_name) do |filename|
+
         sheet    = workbook.worksheet sheet
 
         rows = []
@@ -156,8 +165,17 @@ module TSV
       text = Misc.process_options options, :text
 
       header = true unless header == false
-      TmpFile.with_file do |filename|
-        workbook = RubyXL::Parser.parse file
+
+      sheet ||= "0"
+      workbook = RubyXL::Parser.parse file
+      if sheet &&  sheet =~ /^\d+$/
+        sheet = workbook.worksheets.collect{|s| s.sheet_name }[sheet.to_i]
+      end
+      sheet_name = sheet
+      Log.debug "Opening XLSX #{file} sheet #{ sheet_name }"
+
+      TmpFile.with_file :extension => Misc.sanitize_filename(sheet_name) do |filename|
+
         sheet    = sheet ? workbook[sheet] : workbook.worksheets.first
 
         rows = []

data/lib/rbbt/tsv/util.rb

@@ -328,6 +328,7 @@ module TSV
     end
     self.annotate(new)
     new.type = :single
+    new.fields = [new.fields.first] if new.fields.length > 1
     new
   end
 

data/lib/rbbt/util/misc/omics.rb

@@ -167,7 +167,7 @@ module Misc
     while ref.length >= 1 and muts.reject{|m| m[0] == ref[0]}.empty?
       ref = ref[1..-1]
       raise "REF nil" if ref.nil?
-      pos = pos + 1
+      pos = pos + 1 unless ref.empty?
       muts = muts.collect{|m| m[1..-1]}
     end
 

data/share/Rlib/svg.R

@@ -19,7 +19,7 @@ rbbt.SVG.extract <- function(plot, size=NULL, prefix=NULL, ...){
         base.size = 10 * (7/size)
         resolution = 72 * (size/7)
 
-        if (length(plot$theme) == 0) plot <- plot + theme_gdocs();
+        if (length(plot$theme) == 0) plot <- plot + theme_light();
         if (length(plot$theme$text) == 0) plot <- plot + theme(text = element_text(size=base.size));
 
         plot$theme$text$size = base.size

data/share/rbbt_commands/rsync

@@ -42,6 +42,5 @@ if options[:print]
   puts cmd 
   exit 0
 else
-  io = CMD.cmd(cmd, :log => true, :pipe => true)
-  Misc.consume_stream(io, false, STDOUT)
+  CMD.cmd_log(cmd)
 end

data/share/rbbt_commands/workflow/task

@@ -106,7 +106,7 @@ def fix_options(workflow, task, job_options)
                 end
               end
             when :array
-              if input_options[name] and input_options[name][:stream] and String === value and Misc.is_filename? value
+              if input_options[name] and input_options[name][:stream] and String === value and Misc.is_filename?(value) and not input_options[name][:nofile]
                 get_value_stream(value)
               elsif input_options[name] and input_options[name][:stream] and value == "-"
                 STDIN
@@ -119,7 +119,7 @@ def fix_options(workflow, task, job_options)
                         when value == '-'
                           array_separator ||= "\n"
                           STDIN.read
-                        when (String === value and File.exist?(value))
+                        when (String === value and File.exist?(value) and not input_options[name][:nofile])
                           array_separator ||= "\n"
                           Open.read(value)
                         else

data/test/rbbt/tsv/test_accessor.rb

@@ -222,6 +222,20 @@ row2    aa|aa|AA|AA    b1|b2|B1|B2    Id1|Id1|Id2|Id2
     end
   end
 
+  def test_to_s_unmerge_expand
+    content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|A    b|B    Id1
+row2    aa|aa|AA|AA    b1|b2|B1|B2    Id2
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/)
+      text = tsv.to_s(nil, false, :expand)
+      assert text =~ /row2\taa\tb2\tId2/
+    end
+  end
+
   def test_remove_duplicates
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID

data/test/rbbt/util/test_misc.rb

@@ -428,6 +428,10 @@ eum fugiat quo voluptas nulla pariatur?"
     assert_equal [737407, ["-----", "-----G", "-----GTTAAT"]], Misc.correct_vcf_mutation(737406, "GTTAAT", "G,GG,GGTTAAT")
   end
 
+  def test_mutation_to_ensembl_format
+    assert_equal Misc.mutation_to_ensembl_format("1:100:T", "A"), %w(1 100 100 A/T)
+  end
+
   def test_fingerprint
     assert_equal '{:a=>1}', Misc.fingerprint({:a => 1})
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.130
+  version: 5.21.131
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-06-11 00:00:00.000000000 Z
+date: 2018-06-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake