indentation-example.lisp

; Lispworks

(defun fastq-reader (fname)
  (let ((in (open fname)))
    #'(lambda ()
	(prog2  ; <-- prog1 and prog2 are nifty!
	    (read-line in nil)
	    (read-line in nil)  ; <-- this is the sequence line
	  (read-line in nil)
	  (read-line in nil)))))

(defparameter gen (fastq-reader "../../DATA/sm_r1.fq"))
(loop for seq = (funcall gen) ; <-- Note this
      while seq do (format t "~A~%" seq))


(defun kmer-gen (seq &key (kmer-size 30) (discard-N? nil))
  (let ((n 0) (n-max (- (length seq) kmer-size)))
    #'(lambda ()
	(prog1
	    (if (< n n-max)
		(subseq seq n (+ n kmer-size))
              nil)
	  (incf n)))))

(defparameter gen (fastq-reader "../../DATA/sm_r1.fq"))
(loop for seq = (funcall gen)
      while seq do
      (let ((g (kmer-gen seq :kmer-size 10)))
        (loop for s = (funcall g)
              while s do (format t "~A~%" s))))



; GNU Emacs / SLIME

(defun fastq-reader (fname)
  (let ((in (open fname)))
    #'(lambda ()
	(prog2  ; <-- prog1 and prog2 are nifty!
	    (read-line in nil)
	    (read-line in nil)  ; <-- this is the sequence line
	  (read-line in nil)
	  (read-line in nil)))))

(defparameter gen (fastq-reader "../../DATA/sm_r1.fq"))
(loop for seq = (funcall gen) ; <-- Note this
   while seq do (format t "~A~%" seq))


(defun kmer-gen (seq &key (kmer-size 30) (discard-N? nil))
  (let ((n 0) (n-max (- (length seq) kmer-size)))
    #'(lambda ()
	(prog1
	    (if (< n n-max)
		(subseq seq n (+ n kmer-size))
		nil)
	  (incf n)))))

(defparameter gen (fastq-reader "../../DATA/sm_r1.fq"))
(loop for seq = (funcall gen)
   while seq do
     (let ((g (kmer-gen seq :kmer-size 10)))
       (loop for s = (funcall g)
	  while s do (format t "~A~%" s))))