Class: HansenLab::Tasks::FlagRow

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

Overview

:startdoc::manifest flag rows in a table Flags rows in a table that have a column matching a specified regexp pattern. You can specify the column to check by name (in which case the first row is assumed to be headers) or by number (starting with column 0). Patterns are matched without regard to case.

Examples:

# match the 'accession' column with entries like 'mouse'
% tap run -- flag_row FILE --column accession --pattern mouse

# match the first (ie index == 0) column with entries
# like 'a mouse' or 'a human'
% tap run -- flag_row FILE --column 0 --pattern "a mouse|a human"

Instance Method Summary collapse

Instance Method Details

#flag_rows(table) ⇒ Object 



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# File 'lib/hansen_lab/tasks/flag_row.rb', line 28

def flag_rows(table)
  column_index = case check_column
  when String then table.headers.index(check_column)
  when Integer then check_column
  else nil
  end

  if column_index == nil  || table.n_columns <= column_index
    raise "could not identify column: #{check_column}"
  end
  
  # iterate over the rows and add a flag signaling
  # a match to the pattern
  table.data.collect! do |row|
    row << (row[column_index] =~ pattern ? flag : no_flag)
  end
  
  table
end

#process(target, source) ⇒ Object

process defines what the task does; use the same number of inputs to enque the task as specified here



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# File 'lib/hansen_lab/tasks/flag_row.rb', line 51

def process(target, source)
  
  log_basename :process, source
  
  # load the data and split into rows
  table = parse_table(File.read(source))
  flag_rows(table)

  # prepare the target file and dump the results
  prepare(target) 
  File.open(target, "wb") do |file|
    file << table.join(row_sep, col_sep, header_row)
  end
  
  target
end