16331fb57509 default tip

--- a/stumpwm/bioinf.lisp	Thu Jan 30 09:44:14 2025 -0500
+++ b/stumpwm/bioinf.lisp	Wed Feb 05 11:30:40 2025 -0500
@@ -13,3 +13,40 @@
 (defcommand random-dna (n) ((:integer "Length: "))
   (pbcopy (random-dna-string n)))
 
+(defun random-fasta-string (entries entry-length)
+  (str:join #\newline
+            (loop :for i :from 0 :below entries
+                  :collect (format nil ">seq ~D" i)
+                  :collect (random-dna-string entry-length))))
+
+(defcommand random-fasta
+    (entries entry-length)
+    ((:integer "Entries: ")
+     (:integer "Entry Length: "))
+  (check-type entries (integer 1 *))
+  (check-type entry-length (integer 1 *))
+  (pbcopy (random-fasta-string entries entry-length)))
+
+
+(defun kmers-of (k seq)
+  (loop :for start :from 0
+        :for end :from k :to (length seq)
+        :collect (subseq seq start end)))
+
+(defun kmerized-string (k seq)
+  (with-output-to-string (s)
+    (loop :for i :from 0
+          :for kmer :in (kmers-of k seq)
+          :do (format s "~,,V,@A~%" i kmer))))
+
+(defcommand kmerize (k) ((:integer "k: "))
+  (pbcopy (kmerized-string k (pbpaste))))
+
+
+#; Scratch --------------------------------------------------------------------
+
+(random-fasta-string 10 100)
+
+(format nil "~,,99,@A" "hello")
+
+(kmers-of 3 "ACTTAC")