Class: HansenLab::Tasks::AlignColumns

Inherits:
Tap::Tasks::TableTask
  • Object
show all
Defined in:
lib/hansen_lab/tasks/align_columns.rb

Overview

startdoc::manifest align table data across multiple files Aligns the table data across multiple files. Takes a list of tab-delimited input files.

Instance Method Summary collapse

Instance Method Details

#format_row(data) ⇒ Object 



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# File 'lib/hansen_lab/tasks/align_columns.rb', line 15

def format_row(data)
  data.join(col_sep * 2) + row_sep
end

#process(target, *filepaths) ⇒ Object 



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# File 'lib/hansen_lab/tasks/align_columns.rb', line 19

def process(target, *filepaths)
    
  # load the table data
  tables = filepaths.collect do |filepath|
    log_basename :align, filepath
    parse_table(File.read(filepath))
  end
  
  # hash rows by the sorting keys
  sorting_keys = []
  key_hashes = tables.collect do |table|
    
    keys = case sort_column
    when Integer then table.column(sort_column)
    when String then table.column_by_header(sort_column)
    end
    
    hash = {}
    keys.each_with_index do |key, i|
      (hash[key] ||= []) << i
    end
    sorting_keys.concat(keys)
    
    hash
  end
  
  # sort, omitting empty keys
  sorting_keys = sorting_keys.uniq.sort.delete_if do |key|
    key.strip.empty?
  end
  
  # normalize the number of rows for each key, cross table
  sorting_keys.each do |key|
    max = key_hashes.inject(0) do |max, hash|
      row_index = (hash[key] ||= [])
      row_index.length > max ? row_index.length : max
    end
    
    key_hashes.each do |hash|
      row_index = hash[key]
      row_index.concat Array.new(max - row_index.length, nil)
    end
  end
  
  # prepare the target file and dump the results
  prepare(target) 
  File.open(target, "wb") do |file|
    # print file header
    header = []
    filepaths.each_with_index do |filepath, i|
      table = tables[i]
      unless table.n_columns == 0
        array = table.blank_row
        array[0] = "# #{File.basename(filepath)}"
        header << array.join(col_sep)
      end
    end
    file.print format_row(header)
    
    # print header if applicable
    if header_row
      row = tables.collect {|table| table.headers.join(col_sep)}
      file.print format_row(row)
    end
    
    sorting_keys.each do |key|
      key_rows = []
      tables.each_with_index do |table, index|
        row_index = key_hashes[index][key]
        rows = row_index.collect do |i| 
          (i == nil ? table.blank_row : table.data[i]).join(col_sep)
        end
        
        key_rows << rows
      end
    
      key_rows.transpose.collect do |row|
        file.print format_row(row)
      end
    end
  end
  
  target
end