Find and replace csv strings using a list in python

Question

I have this so far.

import csv

ifile = open('file', 'rb')
reader = csv.reader(ifile,delimiter='\t')
ofile = open('file', 'wb')
writer = csv.writer(ofile, delimiter='\t')


findlist = ['A', 'G', 'C', 'T', 'Y', 'R', 'W', 'S', 'K', 'M', 'X', 'N', '-']
replacelist = ['AA', 'GG', 'CC', 'TT', 'CT', 'AG', 'AT', 'GC', 'TG', 'CA', 
'NN', 'NN', '-']

rep = dict(zip(findlist, replacelist))

def findReplace(find, replace):
    s = ifile.read()
    s = s.replace(find, replace)
    ofile.write(s)

for item in findlist:
    findReplace(item, rep[item])

ifile.close()
ofile.close()

What it does is replaced the A with AA. However what I want is to replace all of the letters with the ones in the replacelist. I am very new to python and can't quite figure out why its not replacing everything.

HE670865    399908  N   N   N   N   N
HE670865    399910  N   N   N   N   N
HE670865    399945  T   T   N   T   T
HE670865    399951  R   R   N   A   A
HE670865    399957  A   A   N   A   A
HE670865    399978  C   C   C   M   C
HE670865    399980  C   C   C   C   C
HE670865    399982  T   T   T   T   K
HE670865    399984  C   C   C   C   C


HE670865    399908  N   N   N   N   N
HE670865    399910  N   N   N   N   N
HE670865    399945  T   T   N   T   T
HE670865    399951  R   R   N   AA  AA
HE670865    399957  AA  AA  N   AA  AA
HE670865    399978  C   C   C   M   C
HE670865    399980  C   C   C   C   C
HE670865    399982  T   T   T   T   K
HE670865    399984  C   C   C   C   C

Paul Draper · Accepted Answer · 2013-11-03 00:55:55Z

6

It is because you are reading and writing inside the loop.

rep = dict(zip(findlist, replacelist))

s = ifile.read()
for item in findlist:
    s = s.replace(item, rep[item])
ofile.write(s)

Also, I think your code would be more readable (and more concise), without using the unnecessary dict.

s = ifile.read()
for item, replacement in zip(findlist, replacelist):
    s = s.replace(item, replacement)
ofile.write(s)

answered Nov 3, 2013 at 0:55

Paul Draper

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2 Comments

shad0w_wa1k3r Over a year ago

I didn't get the reason for the question code not working. Was it because of the function usage resulting in localized variables? I tried with ifile & ofile as strings & that was the error in my code.

Paul Draper Over a year ago

Since you read and wrote for every replace, ifile had already been read all the way to the end after the first iteration. So ifile.read() was returning the empty string after the first iteration.

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