module Mspire::Ident::PeptideHit::Qvalue

Constants

FILE_DELIMITER
FILE_EXTENSION

Public Class Methods

from_file(filename) click to toggle source

returns an array of PeptideHit objects from a phq.tsv

# File lib/mspire/ident/peptide_hit/qvalue.rb, line 35
def from_file(filename)
  searches = Hash.new {|h,id|  h[id] = Mspire::Ident::Search.new(id) }
  peptide_hits = []
  File.open(filename) do |io|
    header = io.readline.chomp.split(FILE_DELIMITER)
    raise "bad headers" unless header == HEADER 
    io.each do |line|
      line.chomp!
      (run_id, id, aaseq, charge, qvalue) = line.split(FILE_DELIMITER)
      ph = Mspire::Ident::PeptideHit.new
      ph.search = searches[run_id]
      ph.id = id; ph.aaseq = aaseq ; ph.charge = charge.to_i ; ph.qvalue = qvalue.to_f
      peptide_hits << ph
    end
  end
  peptide_hits
end
Also aliased as: from_phq
from_phq(filename)
Alias for: from_file
to_file(filename, hits, qvalues=[]) click to toggle source

writes the peptide hits to a phq.tsv file. qvalues is a parallel array to hits that can provide qvalues if not inherent to the hits returns the filename. Expects each hit to implement search_id, id, aaseq and charge. returns the filename

# File lib/mspire/ident/peptide_hit/qvalue.rb, line 24
def to_file(filename, hits, qvalues=[])
  File.open(filename,'w') do |out|
    out.puts HEADER.join(FILE_DELIMITER)
    hits.zip(qvalues) do |hit, qvalue|
      out.puts [hit.search_id, hit.id, hit.aaseq, hit.charge, qvalue || hit.qvalue].join(FILE_DELIMITER)
    end
  end
  filename
end
to_phq(base, hits, qvalues=[]) click to toggle source

writes to the file, adding an extension. returns the filename

# File lib/mspire/ident/peptide_hit/qvalue.rb, line 16
def to_phq(base, hits, qvalues=[])
  to_file(base + FILE_EXTENSION, hits, qvalues)
end