Python find and replace script doing incomplete job -


from answer previous question (efficient means of mass converting >600,000 different find , replaces within 1 file), received bit of python code 1000s of find/replaces en masse.

the code worked then, trying use conduct ~20,000 find/replaces on second column of table looks this:

1   1:565596    0   565596 1   1:567137    0   567137 1   rs7419119   0   842013 1   rs13302957  0   891021 1   rs6696609   0   903426 1   rs8997  0   949654

there 600,000 lines in overall table. these values colons (e.g., 1:565596) need replaced other values. each substitution needed on once in data table. have substitution table looks similar 1 used before. 

coordinate  affy_snp_id 17:4744823  affx-14001316 1:8362754   affx-14761301 3:128686912 affx-21139873 8:11830502  affx-31417216 12:23201352 affx-7455925

the adapted code above implemented such

import csv  subs = dict(csv.reader(open('coordtoaffy.txt'), delimiter='\t')) source = csv.reader(open('neanderthal.map'), delimiter='\t') dest = csv.writer(open('neanderthal-affy.map', 'wb'), delimiter='\t')  row in source:     row[1] = subs.get(row[1], row[1])     dest.writerow(row)

the code worked before (in question linked above), in case only completing small subset of required substitutions. have input on how fix this? thanks!


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