clojure - 改进用于迭代文本解析的 clojure 延迟序列的使用

Question

我正在编写 this coding challenge 的 Clojure 实现，试图找到 Fasta 格式的序列记录的平均长度:

>1
GATCGA
GTC
>2
GCA
>3
AAAAA

有关更多背景，请参阅此 related StackOverflow post关于 Erlang 解决方案。

我的初学 Clojure 尝试使用惰性序列尝试一次读取文件一条记录，以便它可以扩展到大文件。然而，它相当消耗内存且速度缓慢，所以我怀疑它没有以最佳方式实现。这是使用 BioJava 的解决方案抽象出记录解析的库:

(import '(org.biojava.bio.seq.io SeqIOTools))
(use '[clojure.contrib.duck-streams :only (reader)])

(defn seq-lengths [seq-iter]
  "Produce a lazy collection of sequence lengths given a BioJava StreamReader"
  (lazy-seq
    (if (.hasNext seq-iter)
      (cons (.length (.nextSequence seq-iter)) (seq-lengths seq-iter)))))

(defn fasta-to-lengths [in-file seq-type]
  "Use BioJava to read a Fasta input file as a StreamReader of sequences"
  (seq-lengths (SeqIOTools/fileToBiojava "fasta" seq-type (reader in-file))))

(defn average [coll]
  (/ (reduce + coll) (count coll)))

(when *command-line-args*
  (println
    (average (apply fasta-to-lengths *command-line-args*))))

以及没有外部库的等效方法:

(use '[clojure.contrib.duck-streams :only (read-lines)])

(defn seq-lengths [lines cur-length]
  "Retrieve lengths of sequences in the file using line lengths"
  (lazy-seq
    (let [cur-line (first lines)
          remain-lines (rest lines)]
      (if (= nil cur-line) [cur-length]
        (if (= \> (first cur-line))
          (cons cur-length (seq-lengths remain-lines 0))
          (seq-lengths remain-lines (+ cur-length (.length cur-line))))))))

(defn fasta-to-lengths-bland [in-file seq-type]
  ; pop off first item since it will be everything up to the first >
  (rest (seq-lengths (read-lines in-file) 0)))

(defn average [coll]
  (/ (reduce + coll) (count coll)))

(when *command-line-args*
  (println
    (average (apply fasta-to-lengths-bland *command-line-args*))))

当前的实现在一个大文件上需要 44 秒，而 Python 实现需要 7 秒。您能否提供有关加快代码速度并使其更直观的任何建议？使用lazy-seq是否按预期正确解析文件记录？

Answer 1

可能没关系，但是average捕获了长度序列的头部。
以下是一种完全未经测试但更懒惰的方式来做我认为你想做的事情。

(use 'clojure.java.io) ;' since 1.2

(defn lazy-avg [coll]
  (let [f (fn [[v c] val] [(+ v val) (inc c)])
        [sum cnt] (reduce f [0 0] coll)]
    (if (zero? cnt) 0 (/ sum cnt)))

(defn fasta-avg [f]
  (->> (reader f) 
    line-seq
    (filter #(not (.startsWith % ">")))
    (map #(.length %))
    lazy-avg))