require "pasv_lib/version" require File.join __dir__, "..", "vendor", "systemu" module PasvLib module CoreExtensions module Time def date_and_time fmt="%F %T.%L" Object::Time.now.strftime fmt end def time_it title="", logger=nil, run: true if run t = Object::Time.now yield time = Object::Time.now - t if title == "" msg = "Finished in #{time} seconds" else msg = "#{title} finished in #{time} seconds" end if logger logger.info msg else $stderr.puts msg end end end end module Process include CoreExtensions::Time def run_it *a, &b exit_status, stdout, stderr = SystemUniversal::Run.systemu *a, &b puts stdout unless stdout.empty? unless stderr.empty? || stderr.include?("Insecure world writable dir") $stderr.puts stderr end exit_status end def run_it! *a, &b exit_status = self.run_it *a, &b # Sometimes, exited? is not true and there will be no exit # status. Success should catch all failures. AbortIf.abort_unless exit_status.success?, "Command failed with status " + "'#{exit_status.to_s}' " + "when running '#{a.inspect}', " + "'#{b.inspect}'" exit_status end # Examples # # Process.extend CoreExtensions::Process # Time.extend CoreExtensions::Time # # Process.run_and_time_it! "Saying hello", # %Q{echo "hello world"} # # Process.run_and_time_it! "This will raise SystemExit", # "ls arstoeiarntoairnt" do # puts "i like pie" # end def run_and_time_it! title="", cmd="", logger=AbortIf::logger, &b AbortIf.logger.debug { "Running: #{cmd}" } time_it title, logger do run_it! cmd, &b end end end end module Utils # @note Takes 1-based coordinates. def spans_start query_seq, gapped_start !query_seq[0..gapped_start-1].tr("-", "").empty? end # @note Takes 1-based coordinates. def spans_end query_seq, gapped_end !query_seq[gapped_end-1..query_seq.length-1].tr("-", "").empty? end # @note Returns a hash that accepts and returns 1-based coordinates. def pos_to_gapped_pos gapped_key_seq pos_to_gapped_pos = {} nongap_idx = 0 gapped_key_seq.each_char.with_index do |char, gapped_idx| unless char == "-" pos_to_gapped_pos[nongap_idx + 1] = (gapped_idx + 1) nongap_idx += 1 end end pos_to_gapped_pos end # @note The key posns are 1-based and non-gapped. The query seq # is gapped. def get_oligo gapped_query_seq, key_posns, pos_to_gapped_pos gapped_key_posns = key_posns.map do |pos| pos_to_gapped_pos[pos] end gapped_key_posns.map do |pos| idx = pos - 1 gapped_query_seq[idx] end.join.upcase end def get_type oligo, spans if spans == "NA" oligo else "#{oligo}_#{spans}" end end end end