;; (load "~/src/lsw/trunk/bug/iAF1261/ecocyc-ucsd-cpd-map.lisp")
;; (load "~/src/lsw/trunk/bug/iAF1261/rxns-with-unmapped-cpds.lisp")
;; (make-rxn-map-by-gene "~/src/lsw/trunk/bug/iAF1261/other-rxn-mappings-by-gene.txt" (get-rxns-of-blattners *rxns-with-unmapped-cpds*) *ecocyc-ucsd-cpds*)

(defun print-comments-of-protein-by-blattner (unmatched-genes name)
  (format t "~A = {" name)
  (loop for rxn-genes in unmatched-genes
	for rxn = (first rxn-genes)
	for blattners = (second rxn-genes)
	do (loop for blattner in blattners
		 for gene = (find-gene-by-blattner blattner)
		      when (not (reactions-of-gene gene))
		      do   (loop for product in (all-products-of-gene gene)
				 do (format t "('~A', '~A') :  \"\"\"~A\"\"\",~%"  blattner rxn (get-slot-values product 'comment)))))
  (format t "}~%"))



(defun print-ecocyc-rxns-and-comments-of-gene-to-python (ucsd-rxns-of-genes python-dir name)
  (tofile (format nil "~A/~A.py" python-dir name) 
    (format t "~A = {" name)
    (loop for ucsd-rxns-of-gene in ucsd-rxns-of-genes
	  for blattner = (first ucsd-rxns-of-gene)
	  for gene = (find-gene-by-blattner blattner)
	  for ucsd-rxns = (second ucsd-rxns-of-gene)
	  
	  do (format t "'~A' : {'ecocyc-rxns': {" blattner )
	  (loop for rxn in (reactions-of-gene gene)
		do (format t "\"\"\"~A\"\"\": \"\"\"~A\"\"\"," rxn (get-name-string rxn :rxn-eqn-as-name? t)))
	  (format t "},'ucsd-rxns' : [")
	  (loop for rxn in ucsd-rxns
		do (format t "'~A'," rxn))
	  (format t "], 'protein-comments' : [")
	  (loop for product in (all-products-of-gene gene)
		do (format t "\"\"\"~A\"\"\"," (get-slot-values product 'comment )))
	  (format t "]},~%"))
    (format t "}~%")))


(defun print-reactions-of-protein-by-blattner (unmatched-genes ecocyc-ucsd-cpds)
  (format t "blattner	ecogene	ucsd-rxn	ecocyc-rxn	ecocyc-eqn	ecocyc-substrates~%")
  (loop for rxn-genes in unmatched-genes
	for rxn = (first rxn-genes)
	for blattners = (second rxn-genes)
	do (loop for blattner in blattners
		 for gene = (find-gene-by-blattner blattner)
		      when (reactions-of-gene gene)
		      do (loop for ecocyc-rxn in (reactions-of-gene gene)
				   do (format t "~A	~A	~A	~A	~A	~{~A,~}~%" 
					      blattner gene rxn ecocyc-rxn 
					      (get-name-string ecocyc-rxn :strip-html? t) 
					      (get-ucsd-cpds (substrates-of-reaction ecocyc-rxn) ecocyc-ucsd-cpds))))))

(defun find-gene (gene)
  (get-substring-matches '|Genes| gene))

(defun find-gene-by-blattner (blattner)
  (let ((gene (find-gene blattner)))
    (if gene (caar gene))))


(defun make-rxn-map-by-gene (filename rxns-of-genes ecocyc-ucsd-cpds)
  (tofile filename
    (progn 
      (format t "blattner	ecogene	ucsd-rxn	ecocyc-rxn	ecocyc-eqn	ecocyc-substrates~%")
      (loop for entries in rxns-of-genes 
	    do (loop for entry in entries
		     for blattner = (first entry)
		     for ecogene = (second entry)
		     for ucsd-rxn = (third entry)
		     for biocyc-rxns =  (fourth entry)
		     when biocyc-rxns
		     do (loop for rxn in biocyc-rxns
			      for rxn-frame = (first rxn)
			      for substrates = (second rxn)
			      for rxn-eqn = (third rxn)
			      do (format t "~A	~A	~A	~A	~A	~{~A,~}~%" 
					 blattner ecogene ucsd-rxn rxn-frame rxn-eqn (mapcar #'(lambda (x) (if (gethash x ecocyc-ucsd-cpds)
													       (gethash x ecocyc-ucsd-cpds)
													       x)) substrates))))))))
  
(defun get-ucsd-cpds (substrates ecocyc-ucsd-cpds)
  (loop for substrate in substrates
	collect (if (gethash substrate ecocyc-ucsd-cpds)
	       (gethash substrate ecocyc-ucsd-cpds)
	       substrate)))

(defun get-rxns-of-blattners (unmatched-genes)
  (loop for unmatched-gene in unmatched-genes
	  for ucsd-rxn = (first unmatched-gene)
	  for blattners = (second unmatched-gene)
	  collect (loop for blattner in blattners
			for gene = (find-gene-by-blattner blattner)
			when gene
			collect (list blattner 
				      gene 
				      ucsd-rxn 
				      (loop for rxn in (reactions-of-gene gene) 
					    collect (list rxn (substrates-of-reaction rxn) (get-name-string rxn :rxn-eqn-as-name? t :strip-html? t)))))))


(defun match-rxns-by-gene (lispdir category genes-of-ucsd-rxn ecocyc-ucsd-cpds)
  (tofile (format nil  "~A/~A-ecocyc-rxns-of-gene.txt" lispdir category) 
    (print-reactions-of-protein-by-blattner genes-of-ucsd-rxn ecocyc-ucsd-cpds))
  (tofile (format nil "~A/~A-ecocyc-comments-of-gene.py" lispdir category) 
    (print-comments-of-protein-by-blattner genes-of-ucsd-rxn 
					   (format nil "~A_ecocyc_comments_of_gene" category))))