evolution

Author: tmoerman

README.md

@@ -1,2 +1,3 @@
 rosalind
-========
+=======
+

doc/intro.md

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+# Introduction to rosalind
+
+TODO: write [great documentation](http://jacobian.org/writing/great-documentation/what-to-write/)

project.clj

@@ -1,6 +1,7 @@
 (defproject rosalind "0.1.0-SNAPSHOT"
-  :description "FIXME: write description"
-  :url "http://example.com/FIXME"
+  :description "Project Rosalind problems in Clojure"
+  :url "http://github.com/tmoerman/rosalind"
   :license {:name "Eclipse Public License"
             :url "http://www.eclipse.org/legal/epl-v10.html"}
-  :dependencies [[org.clojure/clojure "1.5.1"]])
+  :dependencies [[org.clojure/clojure "1.5.1"]]
+  :main rosalind.core)

src/rosalind/core.clj

@@ -1,6 +1,5 @@
-(ns rosalind.core)
+(ns rosalind.core
+   (:gen-class))
 
-(defn foo
-  "I don't do a whole lot."
-  [x]
-  (println x "Hello, World!"))
+(defn -main [& args]
+  (prn "Project Rosalind in Clojure"))

src/rosalind/dna.clj

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+(ns rosalind.dna
+  (:use clojure.java.io)
+  (:use [clojure.string :only (trim)]))
+
+;;
+;; http://rosalind.info/problems/dna/
+;;
+
+(def dna-data (trim (slurp (resource "rosalind_dna.txt"))))
+
+(defn freqs [collection] (vals (sort (frequencies collection))))
+
+(freqs dna-data)

src/rosalind/fasta.clj

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+(ns rosalind.fasta
+  (:use [clojure.string :only (join trim)]))
+
+;; 
+;; fasta related functions
+;;
+
+(defn is-fasta-header-line [line] (.startsWith line ">"))
+
+(def is-fasta-seq-line (complement is-fasta-header-line))
+
+(defn join-trimmed [strings] (join (map trim strings)))
+
+(defn parse-fasta
+  "parses a fasta file to a seq of maps {:header \"header\" :seq \"AAACTGCCA\"}"
+  [lines]
+  (let [step (fn [c]
+               (when-let [s (seq c)]
+                 (let [fasta-header-line (.substring (first s) 1)
+                       [fasta-seq-lines fasta-rest] (split-with is-fasta-seq-line (rest s))]
+                   (cons {:header fasta-header-line
+                          :seq    (join-trimmed fasta-seq-lines)} 
+                         (parse-fasta fasta-rest)))))]
+    (lazy-seq (step lines))))

src/rosalind/gc.clj

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+(ns rosalind.gc
+  (:use clojure.java.io)
+  (:use rosalind.fasta))
+
+;;
+;; http://rosalind.info/problems/gc/
+;;
+
+(defn nucleotide-count [dna-string & nucleotides]
+  (let [freqs (frequencies dna-string)]
+    (reduce + (map freqs nucleotides))))
+
+(defn nucleotide-ratio [dna-string & nucleotides]
+  (/ (apply nucleotide-count dna-string nucleotides) (count dna-string)))
+
+(defn gc-ratio [dna-string] (nucleotide-ratio dna-string \C \G))
+
+(defn gc-pct [dna-string] (float (* 100 (gc-ratio dna-string))))
+
+(defn assoc-gc-val [f fasta-map] 
+  (assoc fasta-map :gc (f (:seq fasta-map)))) 
+
+(defn assoc-gc-vals [f fasta-maps] 
+  (map (partial assoc-gc-val f) fasta-maps))
+
+(defn max-gc [fasta-maps-with-gc] 
+    (apply max-key :gc fasta-maps-with-gc))
+
+(defn gc-result [file] 
+  (with-open [rdr (reader (resource file))]
+    (max-gc (assoc-gc-vals gc-pct (parse-fasta (line-seq rdr))))))
+
+(defn pretty-gc [fasta-map] 
+  (format "%s\n%s" (:header fasta-map) (:gc fasta-map)))
+
+(pretty-gc (gc-result "rosalind_gc.txt"))

src/rosalind/revc.clj

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+(ns rosalind.revc
+  (:use clojure.java.io)
+  (:use [clojure.string :only (trim join)]))
+
+;;
+;; http://rosalind.info/problems/revc/
+;;
+
+(def revc-data (trim (slurp (resource "rosalind_revc.txt"))))
+
+(def dna-complement 
+  {\A \T
+   \C \G
+   \G \C
+   \T \A})
+
+(defn reverse-complement [dna-string] (join (map dna-complement (reverse dna-string))))
+
+(reverse-complement revc-data)

src/rosalind/worksheet1.clj

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+(ns rosalind.fasta-test
+  (:require [clojure.test :refer :all])
+  (:require [rosalind.fasta :refer :all]))
+
+(def test-data 
+  '(">Rosalind_6404"
+    "CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC"
+    "TCCCACTAATAATTCTGAGG"
+    ">Rosalind_5959"
+    "CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT"
+    "ATATCCATTTGTCAGCAGACACGC"
+    ">Rosalind_0808"
+    "CCACCCTCGTGGTATGGCTAGGCATTCAGGAACCGGAGAACGCTTCAGACCAGCCCGGAC"
+    "TGGGAACCTGCGGGCAGTAGGTGGAAT"))
+
+(deftest test-parse-fasta
+  (testing "yields a lazy seq"
+    (is ()))
+    (is (not (realized? (parse-fasta test-data)))))