cmdtabs 0.1.0 → 0.1.2

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: be9484e39d920387ed525ae22efa8bf74ba8c176bcd3fa85cd3094557c320c6d
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+  data.tar.gz: c22e8c790cc8c420e3689d8da0835132bf594304bfd727a91cbf6e224ea6818d
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+  data.tar.gz: a1544b22c6453b2f2112451099eaaf42d274200a8184a28605c7e05731aa94570dfc47960c5ddb438ba7e0738dfb5f11c7670a4f8e34a031399dcdd2954a4b53

data/README.md

@@ -1,5 +1,7 @@
 # Cmdtabs
 
+DEPRECATED PROJECT. MIGRATED TO [python cmdtabs](https://github.com/seoanezonjic/py_cmdtabs)
+
 Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/cmdtabs`. To experiment with that code, run `bin/console` for an interactive prompt.
 
 TODO: Delete this and the text above, and describe your gem

data/Rakefile

@@ -1,12 +1,17 @@
 # frozen_string_literal: true
 
 require "bundler/gem_tasks"
-require "rspec/core/rake_task"
-
-RSpec::Core::RakeTask.new(:spec)
+require "rake/testtask"
 
 require "rubocop/rake_task"
 
 RuboCop::RakeTask.new
 
-task default: %i[spec rubocop]
+Rake::TestTask.new(:test) do |t|
+  t.libs << "test"
+  t.libs << "lib"
+  t.test_files = FileList["test/**/*_test.rb"]
+end
+
+task default: %i[test rubocop]
+

data/TEST_file

@@ -0,0 +1 @@
+sample	initial_total_sequences	initial_read_max_length	initial_read_min_length	initial_%gc

data/bin/aggregate_column_data.rb

@@ -1,6 +1,15 @@
 #! /usr/bin/env ruby
 
+ROOT_PATH = File.dirname(__FILE__)
+$LOAD_PATH.unshift(File.expand_path(File.join(ROOT_PATH, '..', 'lib')))
+
 require 'optparse'
+require 'cmdtabs'
+
+
+#####################################################################
+## OPTPARSE
+######################################################################
 
 options = {}
 OptionParser.new do |opts|
@@ -12,8 +21,8 @@ OptionParser.new do |opts|
   end
 
   options[:col_index] = nil
-  opts.on("-x", "--column_index INTEGER", "Column index (0 based) to use as reference") do |item|
-    options[:col_index] = item.to_i
+  opts.on("-x", "--column_index INTEGER", "Column index (1 based) to use as reference") do |item|
+    options[:col_index] = item.to_i - 1
   end
 
   options[:sep] = ','
@@ -22,8 +31,8 @@ OptionParser.new do |opts|
   end
 
   options[:col_aggregate] = nil
-  opts.on("-a", "--column_aggregate INTEGER", "Column index (0 based) to extract data and join for each id in column index") do |item|
-    options[:col_aggregate] = item.to_i
+  opts.on("-a", "--column_aggregate INTEGER", "Column index (1 based) to extract data and join for each id in column index") do |item|
+    options[:col_aggregate] = item.to_i - 1
   end
 
   opts.on_tail("-h", "--help", "Show this message") do
@@ -33,24 +42,10 @@ OptionParser.new do |opts|
 end.parse!
 
 
-agg_data = {}
-if options[:input] == '-'
-	input = STDIN
-else
-	input = File.open(options[:input])
-end
-input.each do |line|
-	fields = line.chomp.split("\t")
-	key = fields[options[:col_index]]
-	val = fields[options[:col_aggregate]]
-	query = agg_data[key]
-	if query.nil?
-		agg_data[key] = [val]
-	else
-		query << val
-	end
-end
-
-agg_data.each do |key, values|
-	STDOUT.puts "#{key}\t#{values.join(options[:sep])}"
-end
+##################################################################################################
+## MAIN
+##################################################################################################
+
+input_table = load_input_data(options[:input])
+agg_data = aggregate_column(input_table, options[:col_index], options[:col_aggregate], options[:sep])
+write_output_data(agg_data)

data/bin/column_filter.rb

@@ -0,0 +1,87 @@
+#!/usr/bin/env ruby
+
+ROOT_PATH = File.dirname(__FILE__)
+$LOAD_PATH.unshift(File.expand_path(File.join(ROOT_PATH, '..', 'lib')))
+
+require 'find'
+require 'optparse'
+require 'cmdtabs'
+
+
+#################################################################################################
+## INPUT PARSING
+#################################################################################################
+options = {}
+
+optparse = OptionParser.new do |opts|
+        options[:table_file] = nil
+        opts.on( '-t', '--table_file FILE', 'Input tabulated file' ) do |table_file|
+            options[:table_file] = table_file
+        end
+
+        options[:cols_to_show] = nil
+        opts.on( '-c', '--column STRING', 'Column/s to show (1 based). Format: x,y,z..' ) do |column|            
+                options[:cols_to_show] = parse_column_indices(sep = ",", column)
+        end
+
+        options[:col_filter] = nil
+        opts.on( '-f', '--col_filter STRING', 'Select columns where search keywords. Format: x,y,z..' ) do |col_filter|
+                options[:col_filter] =  parse_column_indices(sep = ",", col_filter)
+        end      
+
+        options[:keywords] = nil
+        opts.on( '-k', '--keywords STRING', 'Keywords for select rows. Format: key1_col1&key2_col1%key1_col2&key2_col2' ) do |keywords|
+                options[:keywords] = keywords
+        end
+
+        options[:search_mode] = 'c'
+        opts.on( '-s', '--search STRING', 'c for match in every columns set, s some match in some column. Default c' ) do |search_mode|
+                options[:search_mode] = search_mode
+        end
+
+        options[:match_mode] = 'i'
+        opts.on( '-m', '--match_mode STRING', 'i string must include the keyword, c for fullmatch. Default i') do |match_mode|
+                options[:match_mode] = match_mode
+        end
+
+        options[:separator] = "\t"
+        opts.on( '-p', '--separator STRING', 'Separator used in fields. Default i') do |separator|
+                options[:separator] = separator
+        end
+
+        options[:reverse] = false
+        opts.on( '-r', '--reverse', 'Select not matching' ) do 
+                options[:reverse] = true
+        end
+
+        options[:uniq] = false
+        opts.on( '-u', '--uniq', 'Delete redundant items' ) do 
+                options[:uniq] = true
+        end
+
+        options[:header] = false
+        opts.on( '-H', '--header', 'indicate if files have header' ) do 
+                options[:header] = true
+        end
+
+        # Set a banner, displayed at the top of the help screen.
+        opts.banner = "Usage: column_filter.rb -t tabulated_file \n\n"
+
+        # This displays the help screen
+        opts.on( '-h', '--help', 'Display this screen' ) do
+                puts opts
+                exit
+        end
+
+end 
+optparse.parse!
+
+##################################################################################################
+## MAIN
+##################################################################################################
+abort('Tabulated file not specified') if options[:table_file].nil?
+file_names = Dir.glob(options[:table_file])
+input_files = load_several_files(file_names, options[:separator])
+filtered_table = merge_and_filter_tables(input_files, options)
+write_output_data(filtered_table)
+ 

data/bin/create_metric_table.rb

@@ -1,49 +1,37 @@
 #!/usr/bin/env ruby
 
-metric_file = ARGV[0]
-fixCols = ARGV[1].split(',')
-output = ARGV[2]
-name_tag = fixCols.shift
-fixColNumber = fixCols.length
-
-hash = {}
-
-varTags = []
-File.open(ARGV[0]).each do |line|
-	line.chomp!
-	fields = line.split("\t")
-	name = fields.shift
-	fixFields = fields[0..fixColNumber-1]
-	varFields = fields[fixColNumber..fixColNumber+1]
-	varTags << varFields.first if !varTags.include?(varFields.first)
-
-	query = hash[name]
-	if query.nil?
-		hash[name] = {varFields.first => varFields.last}
-		fixCols.each_with_index do |tag, i|
-			hash[name][tag] = fixFields[i] 
-		end
-	else
-		query[varFields.first] = varFields.last
-	end
-end
-
-metric_table = File.new(output, "w")
-if fixColNumber > 0
-	header="#{name_tag}\t#{fixCols.join("\t")}\t#{varTags.join("\t")}"
-else
-	header="#{name_tag}\t#{varTags.join("\t")}"
-end
-
-metric_table.puts(header)
-allTags = fixCols.concat(varTags)
-hash.each do |name, fields|
- 	array_temp = [name]
- 	allTags.each do |tag|
- 		array_temp << fields[tag]
- 	end
- 	metric_table.puts(array_temp.join("\t"))
-end
-metric_table.close()
-
-
+ROOT_PATH = File.dirname(__FILE__)
+$LOAD_PATH.unshift(File.expand_path(File.join(ROOT_PATH, '..', 'lib')))
+require 'optparse'
+require 'cmdtabs'
+
+
+#####################################################################
+## OPTPARSE
+######################################################################
+
+options = {}
+OptionParser.new do |opts|
+  opts.banner = "Usage: #{File.basename(__FILE__)} [options]"
+
+  options[:corrupted] = nil
+  opts.on("-c", "--corrupted PATH", "File where corrupted metrics are stored") do |path|
+    options[:corrupted] = path
+  end
+
+  opts.on_tail("-h", "--help", "Show this message") do
+    puts opts
+    exit
+  end
+end.parse!
+
+##################################################################################################
+## MAIN
+##################################################################################################
+metric_file = load_input_data(ARGV[0])
+attributes = ARGV[1].split(',')
+samples_tag = attributes.shift
+metric_names, indexed_metrics = index_metrics(metric_file, attributes)
+table_output, corrupted_records = create_table(indexed_metrics, samples_tag, attributes, metric_names)
+write_output_data(table_output, ARGV[2])
+write_output_data(corrupted_records, options[:corrupted]) if !options[:corrupted].nil? && !corrupted_records.empty?

data/bin/desaggregate_column_data.rb

@@ -1,6 +1,14 @@
 #! /usr/bin/env ruby
 
+ROOT_PATH = File.dirname(__FILE__)
+$LOAD_PATH.unshift(File.expand_path(File.join(ROOT_PATH, '..', 'lib')))
 require 'optparse'
+require 'cmdtabs'
+
+
+#####################################################################
+## OPTPARSE
+######################################################################
 
 options = {}
 OptionParser.new do |opts|
@@ -12,8 +20,8 @@ OptionParser.new do |opts|
   end
 
   options[:col_index] = nil
-  opts.on("-x", "--column_index INTEGER", "Column index (0 based) to use as reference") do |item|
-    options[:col_index] = item.to_i
+  opts.on("-x", "--column_index INTEGER", "Column index (1 based) to use as reference") do |item|
+    options[:col_index] = item.to_i - 1
   end
 
   options[:sep] = ","
@@ -28,19 +36,12 @@ OptionParser.new do |opts|
 end.parse!
 
 
-agg_data = {}
-if options[:input] == '-'
-	input = STDIN
-else
-	input = File.open(options[:input])
-end
-input.each do |line|
-	fields = line.chomp.split("\t")
-	target_field = fields[options[:col_index]]
-	target_field.split(options[:sep]).each do |val|
-		record = fields[0..(options[:col_index]-1)] + [val] + fields[(options[:col_index] + 1)..fields.length]
-		#record = fields[0..(options[:col_index] + 1)] + [val] + fields[(options[:col_index] + 1)..fields.length]
-		STDOUT.puts record.join("\t")
-	end
-end
+##################################################################################################
+## MAIN
+##################################################################################################
+
+input_table = load_input_data(options[:input])
+desagg_data = desaggregate_column(input_table, options[:col_index], options[:sep])
+write_output_data(desagg_data)
+
 

data/bin/excel_to_tabular.rb

@@ -0,0 +1,57 @@
+#! /usr/bin/env ruby
+#
+## Script to transform xlsx to tabular file. 
+## By default, selects sheet 1 and column 1.
+
+ROOT_PATH = File.dirname(__FILE__)
+$LOAD_PATH.unshift(File.expand_path(File.join(ROOT_PATH, '..', 'lib')))
+
+require 'optparse'
+require 'cmdtabs'
+require 'xsv'
+
+#######################
+## OPTPARSE
+#######################
+
+options = {}
+OptionParser.new do |opts|
+  opts.banner = "Usage: #{File.basename(__FILE__)} [options]"
+
+  options[:columns2extract] = [0]
+  opts.on("-c", "--columns2extract INTEGER", "Column position to extract (1 based). Default 1") do |data|
+    options[:columns2extract] = parse_column_indices(sep = ",", data)
+  end
+
+  options[:input_file] = nil
+  opts.on("-i", "--input_file PATH", "Input xlsx file") do |path|
+    options[:input_file] = path
+  end
+
+  options[:output_file] = 'table.txt'
+  opts.on("-o", "--output_file PATH", "Output tabular file") do |path|
+    options[:output_file] = path
+  end
+
+  options[:sheet_number] = 0
+  opts.on("-s", "--sheet_number INTEGER", "Sheet number to work with. Default 1") do |data|
+    options[:sheet_number] = data.to_i - 1
+  end
+
+  opts.on_tail("-h", "--help", "Show this message") do
+    puts opts
+    exit
+  end
+
+end.parse! 
+
+#######################
+## MAIN
+#######################
+
+#See https://github.com/martijn/xsv
+
+x = Xsv.open(options[:input_file])
+sheet = x.sheets[options[:sheet_number]].to_a
+storage = extract_columns(sheet, options[:columns2extract])
+write_output_data(storage, options[:output_file])

data/bin/intersect_columns.rb

@@ -1,25 +1,10 @@
 #! /usr/bin/env ruby
 
+ROOT_PATH = File.dirname(__FILE__)
+$LOAD_PATH.unshift(File.expand_path(File.join(ROOT_PATH, '..', 'lib')))
 require 'optparse'
+require 'cmdtabs'
 
-#####################################################################
-## METHODS
-######################################################################
-
-def load_records(file, cols, sep)
-	recs = {}
-	File.open(file).each do |line|
-		fields = line.chomp.split(sep)
-		recs[cols.map{|c| fields[c]}] = true
-	end
-	return recs.keys
-end
-
-def print_recs(recs, sep)
-	recs.each do |rec|
-		puts rec.join(sep)
-	end
-end
 
 #####################################################################
 ## OPTPARSE
@@ -40,13 +25,13 @@ OptionParser.new do |opts|
   end
 
   options[:a_cols] = [0]
-  opts.on("-A", "--a_cols STRING", "Index of columns in base 0 to compare") do |item|
-    options[:a_cols] = item.split(',').map{|n| n.to_i}
+  opts.on("-A", "--a_cols STRING", "Index of columns in base 1 to compare") do |item|
+    options[:a_cols] = parse_column_indices(sep = ",", item)
   end
 
   options[:b_cols] = [0]
-  opts.on("-B", "--b_cols STRING", "Index of columns in base 0 to compare") do |item|
-    options[:b_cols] = item.split(',').map{|n| n.to_i}
+  opts.on("-B", "--b_cols STRING", "Index of columns in base 1 to compare") do |item|
+    options[:b_cols] = parse_column_indices(sep = ",", item)
   end
 
   options[:count] = false
@@ -59,6 +44,11 @@ OptionParser.new do |opts|
     options[:keep] = item
   end
 
+  options[:full] = false
+  opts.on("--full", "Give full record") do |item|
+    options[:full] = true
+  end
+
   options[:sep] = "\t"
   opts.on("-s", "--separator STRING", "column character separator") do |item|
     options[:sep] = item
@@ -70,8 +60,11 @@ OptionParser.new do |opts|
   end
 end.parse!
 
-a_records = load_records(options[:a_file], options[:a_cols], options[:sep])
-b_records = load_records(options[:b_file], options[:b_cols], options[:sep])
+input_data_a = load_input_data(options[:a_file], options[:sep])
+input_data_b = load_input_data(options[:b_file], options[:sep])
+
+a_records, full_a_rec = load_records(input_data_a, options[:a_cols], options[:full])
+b_records, full_b_rec = load_records(input_data_b, options[:b_cols], options[:full])
 
 common = a_records & b_records
 a_only = a_records - common
@@ -82,12 +75,20 @@ if options[:count]
 	puts "c: #{common.length}"
 else
 	if options[:keep] == 'c'
-		print_recs(common, options[:sep])
+    result = common
+    result = common.map{|r| full_a_rec[r] + full_b_rec[r]} if options[:full]
 	elsif options[:keep] == 'a'
-		print_recs(a_only, options[:sep])
+    result = a_only
+    result = a_only.map{|r| full_a_rec[r]} if options[:full]
 	elsif options[:keep] == 'b'
-		print_recs(b_only, options[:sep])
+    result = b_only
+    result = b_only.map{|r| full_a_rec[r]} if options[:full]
 	elsif options[:keep] == 'ab'
-		print_recs(a_only + b_only, options[:sep])
+    if options[:full]
+      a_only = a_only.map{|r| full_a_rec[r]}
+      b_only = b_only.map{|r| full_a_rec[r]}
+    end
+    result = a_only + b_only
 	end
+	write_output_data(result, nil, options[:sep])
 end

data/bin/merge_tabular.rb

@@ -1,41 +1,28 @@
 #! /usr/bin/env ruby
+ROOT_PATH = File.dirname(__FILE__)
+$LOAD_PATH.unshift(File.expand_path(File.join(ROOT_PATH, '..', 'lib')))
 
-parent_table = {}
-table_length = 0
+require 'optparse'
+require 'cmdtabs'
 
-ARGV.each do |file_name|
-	
-	local_length = 0
-	File.open(file_name).each do |line|
-		line.chomp!
-		n_fields = line.count("\t")+1
-		fields = line.split("\t", n_fields).map{|field| 
-			if field == ""
-				'-'
-			else
-				field
-			end
-		}
-		next if fields.count('-') == fields.length #skip blank records
-		id = fields.shift 
-		local_length = fields.length
-		if !parent_table.has_key?(id)
-			parent_table[id] = Array.new(table_length,'-')
-		elsif parent_table[id].length < table_length
-			parent_table[id].concat(Array.new(table_length-parent_table[id].length,'-'))
-		end
-		parent_table[id].concat(fields)
+#####################################################################
+## OPTIONS
+######################################################################
+options = {}
+OptionParser.new do |opts|
+  opts.banner = "Usage: #{File.basename(__FILE__)} [options]"
 
-	end
+  opts.on_tail("-h", "--help", "Show this message") do
+    puts opts
+    exit
+  end
+end.parse!
 
-	table_length += local_length
-	parent_table.each do |id, fields|
-		diference = table_length - fields.length
-		fields.concat(Array.new(diference,'-')) if diference > 0
-	end
 
-end
+##################################################################################################
+## MAIN
+##################################################################################################
 
-parent_table.each do |id, fields|
-	puts id+"\t"+fields.join("\t")
-end
+files = load_files(ARGV)
+merged = merge_files(files)
+write_output_data(merged)

data/bin/standard_name_replacer.rb

@@ -1,6 +1,15 @@
 #! /usr/bin/env ruby
 
+ROOT_PATH = File.dirname(__FILE__)
+$LOAD_PATH.unshift(File.expand_path(File.join(ROOT_PATH, '..', 'lib')))
 require 'optparse'
+require 'cmdtabs.rb'
+
+
+
+#####################################################################
+## OPTPARSE
+######################################################################
 
 options = {}
 OptionParser.new do |opts|
@@ -16,44 +25,47 @@ OptionParser.new do |opts|
 		options[:index_file] = item
 	end
 
+	options[:output_file] = nil
+	opts.on("-o", "--output_file PATH", "Output file ") do |item|
+		options[:output_file] = item
+	end
+
 	options[:input_separator] = "\t"
 	opts.on("-s", "--input_separator STRING", "Separator character") do |item|
 		options[:input_separator] = item
 	end
 
 	options[:columns] = [1]
-	opts.on("-c", "--columns STRING", "Columns indexes, comma separated, to perform the ID translations.") do |item|
-		options[:columns] = item.split(','). map{|i| i.to_i - 1}
+	opts.on("-c", "--columns STRING", "Columns indexes (1 based), comma separated, to perform the ID translations.") do |item|
+    	options[:columns] = parse_column_indices(sep = ",", item)
 	end
 
 	options[:from] = 0
 	opts.on("-f", "--from INTEGER", "Column in index file to take reference value. Default 1. Numeration is 1 based") do |item|
-		options[:from] = item.to_i - 1
+    	options[:from] = item.to_i - 1
 	end
 
 	options[:to] = 1
 	opts.on("-t", "--to INTEGER", "Column in index file to take the value that will be used in substitution. Default 2. Numeration is 1 based") do |item|
-		options[:to] = item.to_i - 1
+    	options[:to] = item.to_i - 1
 	end
 
+	options[:remove_untranslated] = false
+	opts.on("-u", "--remove_untranslated", "Activate this flag for remove the untranslated entries") do 
+		options[:remove_untranslated] = true
+	end
 end.parse!
 
-#Load index
-index = {}
-File.open(options[:index_file]).read.each_line do |line|
-	line.chomp!
-	fields = line.split("\t")
-	index[fields[options[:from]]] = fields[options[:to]]
-end
-
-#Reemplaza nombres
-File.open(options[:input_file]+'_rep','w') do |f| 
-	File.open(options[:input_file]).each do |line|
-		fields = line.chomp.split(options[:input_separator])
-		options[:columns].each do |col|
-			new_string = index[fields[col]]
-			fields[col] = new_string if !new_string.nil?
-		end
-		f.puts fields.join(options[:input_separator])
-	end
-end 
+
+##################################################################################################
+## MAIN
+##################################################################################################
+
+input_index = load_input_data(options[:index_file])
+translation_index = index_array(input_index, options[:from], options[:to])
+
+input_table = load_input_data(options[:input_file], options[:input_separator])
+
+tabular_output_translated, _ = name_replaces(input_table, options[:input_separator], options[:columns], translation_index, options[:remove_untranslated])
+
+write_output_data(tabular_output_translated, options[:output_file], options[:input_separator])