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Versions: 19
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Contents
require 'mspire/ident/search'
require 'mspire/ident/peptide_hit'
module Mspire ; end
module Mspire::Ident ; end
class Mspire::Ident::PeptideHit
module Qvalue
FILE_EXTENSION = '.phq.tsv'
FILE_DELIMITER = "\t"
HEADER = %w(run_id id aaseq charge qvalue)
class << self
# writes to the file, adding an extension. returns the filename
def to_phq(base, hits, qvalues=[])
to_file(base + FILE_EXTENSION, hits, qvalues)
end
# 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
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
# returns an array of PeptideHit objects from a phq.tsv
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
alias_method :from_phq, :from_file
end
end # Qvalue
end # Peptide Hit
Version data entries
19 entries across 19 versions & 1 rubygems