Created
June 19, 2009 22:09
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20090619 Peptide Mass Calculation
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require 'ms/in_silico/digester' | |
require 'ms/fasta/archive' | |
require 'molecules' | |
require 'tap' | |
# PeptideMasses::task | |
# | |
# % rap peptide_masses <fasta_file> | |
# | |
class PeptideMasses < Tap::Task | |
Polypeptide = Molecules::Libraries::Polypeptide | |
UnknownResidueError = Molecules::Libraries::Polypeptide::UnknownResidueError | |
def process(fasta_file) | |
output_dir = fasta_file.chomp(File.extname(fasta_file)) | |
if File.exists?(output_dir) | |
raise "output directory already exists: #{output_dir.inspect}" | |
end | |
FileUtils.mkdir_p(output_dir) | |
Dir.chdir(output_dir) | |
digester = Ms::InSilico::Digester['Trypsin'] | |
targets = [] | |
unknowns = File.open('unknowns', "w") | |
start = Time.now | |
n = 0 | |
m = 0 | |
Ms::Fasta::Archive.open(fasta_file) do |arc| | |
arc.each_str do |entry| | |
header, *seq = entry.split(/\r?\n/) | |
i = 0 | |
digester.digest(seq.join).each do |peptide| | |
begin | |
p = Polypeptide.new(peptide) | |
(targets[p.length] ||= Hash.new(0))[p.mass] += 1 | |
rescue(UnknownResidueError) | |
unknowns.puts "- [#{m}, #{i}]" | |
end | |
i += 1 | |
end | |
n += 1 | |
m += 1 | |
if n == 10000 | |
log :split, "# #{m} of #{arc.length} (#{Time.now - start}s)" | |
puts "- split: #{Time.now - start}" | |
puts " index: #{m}" | |
dump(targets) | |
start = Time.now | |
n = 0 | |
end | |
end | |
end | |
unknowns.close | |
end | |
def dump(targets) | |
start = Time.now | |
puts "- dump: " | |
targets.each_index do |index| | |
next unless masses = targets[index] | |
sum = 0 | |
data = [] | |
masses.each_pair do |mass, n| | |
data << mass | |
data << n | |
sum += n | |
end | |
puts " #{index}: [#{masses.length}, #{sum}]" | |
File.open(index.to_s, "a") do |io| | |
io << data.pack("G*") | |
end | |
end | |
targets.clear | |
end | |
end |
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