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I have code that works perfectly, but it uses too much memory.

Essentially this code takes an input file (lets call it an index, that is 2 column tab-separated) that searches in a second input file (lets call it data, that is 4-column tab separated) for a corresponding term in the 1st column which it then replaces with the information from the index file.

An example of the index is:

amphibian   anm|art|art|art|art
anaconda    anm
aardvark    anm

An example of the data is :

amphibian-n is  green   10
anaconda-n  is  green   2
anaconda-n  eats    mice    1
aardvark-n  eats    plants  1

Thus, when replacing the value in Col 1 of data with the corresponding information from Index, the results are as follows:

anm-n   is  green
art-n   is  green
anm-n   eats    mice
anm-n   eats    plants

I divided the code in steps because the idea is to calculate average of the values given a replaced item (Col 4 in data) of Cols 2 and 3 in the data file. This code takes the total number of slot-fillers in the data file and sums the values which is used in Step 3.

The desired results are the following:

anm second  hello   1.0
anm eats    plants  1.0
anm first   heador  0.333333333333
art first   heador  0.666666666667

I open the same input file many times (i.e. 3 times) in Steps 1, 2 and 3 because I need to create several dictionaries that need to be created in a certain order. However, the bottleneck is definitely between Steps 2 and 3. If I remove the function in Step 2, I can process the entire file (13GB of ram in approx. 30 minutes). However, the necessary addition of Step 2 consumes all memory before beginning Step 3.

Is there a way to optimize how many times I open the same input file?

#!/usr/bin/python
# -*- coding: utf-8 -*-

from __future__ import division
from collections import defaultdict

import datetime

print "starting:",
print datetime.datetime.now()

mapping = dict()

with open('input-map', "rb") as oSenseFile:
    for line in oSenseFile:
        uLine = unicode(line, "utf8")
        concept, conceptClass = uLine.split()
        if len(concept) > 2:  
                mapping[concept + '-n'] = conceptClass


print "- step 1:",
print datetime.datetime.now()

lemmas = set()

with open('input-data', "rb") as oIndexFile:
    for line in oIndexFile:
        uLine = unicode(line, "latin1")
        lemma = uLine.split()[0]
        if mapping.has_key(lemma):
            lemmas.add(lemma)

print "- step 2:",
print datetime.datetime.now()


featFreqs = defaultdict(lambda: defaultdict(float))

with open('input-data', "rb") as oIndexFile:            
    for line in oIndexFile:
        uLine = unicode(line, "latin1")
        lemmaTAR, slot, filler, freq = uLine.split()
        featFreqs[slot][filler] += int(freq)


print "- step 3:",
print datetime.datetime.now()

classFreqs = defaultdict(lambda: defaultdict(lambda: defaultdict(float)))

with open('input-data', "rb") as oIndexFile:            
    for line in oIndexFile:
        uLine = unicode(line, "latin1")
        lemmaTAR, slot, filler, freq = uLine.split()
        if lemmaTAR in lemmas:
            senses = mapping[lemmaTAR].split(u'|')
            for sense in senses:
                classFreqs[sense][slot][filler] += (int(freq) / len(senses)) / featFreqs[slot][filler]
        else:
            pass

print "- step 4:",
print datetime.datetime.now()

with open('output', 'wb') as oOutFile:
    for sense in sorted(classFreqs):
                for slot in classFreqs[sense]:
                        for fill in classFreqs[sense][slot]:
                                outstring = '\t'.join([sense, slot, fill,\
                                                       str(classFreqs[sense][slot][fill])])
                                oOutFile.write(outstring.encode("utf8") + '\n')

Any suggestions on how to optimize this code to process large text files (e.g. >4GB)?

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  • 1
    \$\begingroup\$ Why does anaconda become art in the example? The index maps it to anm. \$\endgroup\$ – Janne Karila Mar 2 '14 at 10:20
  • \$\begingroup\$ anaconda does not become art, you are referring to amphibian that is mapped to art. The example demonstrates that for each possible mapping, the Col. inof in Cols 2 and 3 are repeated. \$\endgroup\$ – owwoow14 Mar 2 '14 at 12:26
  • \$\begingroup\$ The example is still not quite clear, but anyway, perhaps you should use a database. \$\endgroup\$ – Janne Karila Mar 2 '14 at 19:30
  • 3
    \$\begingroup\$ I noticed the same question on stackoverflow.com, which has an accepted answer already. \$\endgroup\$ – Janne Karila Mar 3 '14 at 13:56

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