Reading Huge File in Python

Question

I have a 384MB text file with 50 million lines. Each line contains 2 space-separated integers: a key and a value. The file is sorted by key. I need an efficient way of looking up the values of a list of about 200 keys in Python.

My current approach is included below. It takes 30 seconds. There must be more efficient Python foo to get this down to a reasonable efficiency of a couple of seconds at most.

# list contains a sorted list of the keys we need to lookup
# there is a sentinel at the end of list to simplify the code
# we use pointer to iterate through the list of keys
for line in fin:
  line = map(int, line.split())
  while line[0] == list[pointer].key:
    list[pointer].value = line[1]
    pointer += 1
  while line[0] > list[pointer].key:
    pointer += 1
  if pointer >= len(list) - 1:
    break # end of list; -1 is due to sentinel

Coded binary search + seek solution (thanks kigurai!):

entries = 24935502 # number of entries
width   = 18       # fixed width of an entry in the file padded with spaces
                   # at the end of each line
for i, search in enumerate(list): # list contains the list of search keys
  left, right = 0, entries-1 
  key = None
  while key != search and left <= right:
    mid = (left + right) / 2
    fin.seek(mid * width)
    key, value = map(int, fin.readline().split())
    if search > key:
      left = mid + 1
    else:
      right = mid - 1
  if key != search:
    value = None # for when search key is not found
  search.result = value # store the result of the search

Answer 1

I would use memory-maping: http://docs.python.org/library/mmap.html.
This way you can use the file as if it's stored in memory, but the OS decides which pages should actually be read from the file.

Answer 2

Here is a recursive binary search on the text file

import os, stat

class IntegerKeyTextFile(object):
    def __init__(self, filename):
        self.filename = filename
        self.f = open(self.filename, 'r')
        self.getStatinfo()

    def getStatinfo(self):
        self.statinfo = os.stat(self.filename)
        self.size = self.statinfo[stat.ST_SIZE]

    def parse(self, line):
        key, value = line.split()
        k = int(key)
        v = int(value)
        return (k,v)

    def __getitem__(self, key):
        return self.findKey(key)

    def findKey(self, keyToFind, startpoint=0, endpoint=None):
        "Recursively search a text file"

        if endpoint is None:
            endpoint = self.size

        currentpoint = (startpoint + endpoint) // 2

        while True:
            self.f.seek(currentpoint)
            if currentpoint <> 0:
                # may not start at a line break! Discard.
                baddata = self.f.readline() 

            linestart = self.f.tell()
            keyatpoint = self.f.readline()

            if not keyatpoint:
                # read returned empty - end of file
                raise KeyError('key %d not found'%(keyToFind,))

            k,v = self.parse(keyatpoint)

            if k == keyToFind:
                print 'key found at ', linestart, ' with value ', v
                return v

            if endpoint == startpoint:
                    raise KeyError('key %d not found'%(keyToFind,))

            if k > keyToFind:
                return self.findKey(keyToFind, startpoint, currentpoint)
            else:
                return self.findKey(keyToFind, currentpoint, endpoint)

A sample text file created in jEdit seems to work:

>>> i = integertext.IntegerKeyTextFile('c:\\sampledata.txt')
>>> i[1]
key found at  0  with value  345
345

It could definitely be improved by caching found keys and using the cache to determine future starting seek points.