Class: HansenLab::Tasks::AlignMod

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

Overview

:startdoc::manifest align mascot peptide ids at a modification Aligns Mascot peptide identifications along a modification boundary.

For example:

[input.txt]
AAAQAAA 0.0004000.0 first
QBBBBBQ 0.4000004.0 second

Becomes:

[input.align]
|AAA|Q|AAA|first|
|.|Q|BBBBBQ|second (1)|
|QBBBBB|Q|.|second (2)|

Extra fields can be present in the input file, they will be carried forward to the result file. If a sequence has multiple modifications, each will be listed in the result, as above.

Note that while the results don’t seem terribly well aligned here, they can be turned into a table by using RedCloth (for example by posting the result as a message to Basecamp), or you can modify the output with the configs.

Instance Method Summary collapse

Instance Method Details

#format_row(data) ⇒ Object 



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# File 'lib/hansen_lab/tasks/align_mod.rb', line 37

def format_row(data)
  output_line_format % data.join(output_col_sep)
end

#process(target, source) ⇒ Object 



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# File 'lib/hansen_lab/tasks/align_mod.rb', line 41

def process(target, source)
    
  table = parse_table( File.read(source) )
  
  prepare(target) 
  File.open(target, "wb") do |file|
    
    # handle the header row.  Note that the headers need to be
    # moved around a little to conform to the output format.
    if header_row
      file.puts format_row(["", "", ""] + table.headers[2..-1])
    end
    
    sequence_locations = {}
    table.data.each do |line|
      seq, locator, *identifiers = line

      # checks
      unless locator =~ /^\d\.(\d+)\.\d$/ && seq.length == $1.length
        raise "could not split line correctly: #{line}"
      end
      
      locator = $1
      locations = sequence_locations[seq] ||= []
      split_locations = [] 
      0.upto(locator.length-1) do |index|
        if mod_numbers.include?(locator[index, 1].to_i)
          unless locations.include?(index)
            split_locations << index
            locations << index
          end
        end
      end
      
      split_locations.each_with_index do |location, index|
        data = [
          seq[0...location],
          seq[location, 1],
          seq[location+1..-1],
        ] 
        data += identifiers if index == 0
        
        # modify the lead identifier to note duplicates
        data[3] = "#{identifiers[0]} (#{index + 1})" if split_locations.length > 1
        data.collect! {|str| str.empty? ? output_empty_cell : str }
        
        file.puts format_row(data)
      end
      
    end
  end
  
  target
end