bioworks_to_pepxml.rb in mspire-0.4.2

- old
+ new

@@ -10,10 +10,11 @@
 DEFAULT_PARAMS_FILE = Dir[DEFAULT_PARAMS_GLOB].first
 DEFAULT_MS_MODEL = 'LCQ'
 DEFAULT_MASS_ANALYZER = 'Ion Trap'
 ##############################################################
 
-require 'spec_id/sequest/pepxml'
+#require 'spec_id/sequest/pepxml'  # dies of this guy is called (why???)
+require 'spec_id/proph/pep_summary'  # <- he requests the above...hmmm
 require 'spec_id'
 require 'optparse'
 require 'ostruct'
 require 'fileutils'
 require 'spec_id/srf'