(in-package :cl-user)

(defun each-enzyme-synonyms (function)
  (and (config :enzyme)
       (with-open-file (f (config :enzyme))
	 (loop with collecting = :nothing
	    with id and names and entrez
	    for line = (read-line f nil :eof)
	    until (eq line :eof)
	    do 
	    (when (equal line "///")
	      (when entrez
		(funcall function (mapcar 'car entrez) (regex-replace-all "(^EC )|(\\s{2}.*)" id "") names))
	      (setq collecting :nothing names nil id nil entrez nil))
	    (loop for (field value) in (all-matches line "^([A-Z]*)\\s+(.*)" 1 2)
	       do
	       (cond ((string= field "NAME")
		      (setq collecting :names))
		     ((string= field "ENTRY")
		      (setq id value))
		     ((and (eq collecting :names)
			   (not (string= field "")))
		      (setq collecting :nothing))
		     ((#"matches" value "^HSA:.*")
		      (setq collecting :entrez))
		     ((and (eq collecting :entrez)
			   (#"matches" value "^\\S{3}:.*"))
		      (setq collecting :nothing)))
	       (when (eq collecting :names) 
		 (push  (regex-replace-all ";$" value "") names))
	       (when (eq collecting :entrez)
		 (let ((them (all-matches value "(\\d+)\\((.*?)\\)" 1 2)))
		   (setq entrez (append entrez them)))))))))