module Mspire::Ident::PeptideHit::Qvalue
Constants
- FILE_DELIMITER
- FILE_EXTENSION
- HEADER
Public Class Methods
from_file(filename)
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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
to_file(filename, hits, qvalues=[])
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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=[])
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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