Question

So I have file that with multiple line that look like this (space delimiter file):

A1BG      P04217     VAR_018369  p.His52Arg     Polymorphism  rs893184    -
A1BG      P04217     VAR_018370  p.His395Arg    Polymorphism  rs2241788   -
AAAS      Q9NRG9     VAR_012804  p.Gln15Lys     Disease       -           Achalasia

How do I make dictionary to look for id in second column and store the number (between words) on fourth column.

I tried this but it give me index of out range

lookup = defaultdict(list)
with open ('humsavar.txt', 'r') as humsavarTxt:
    for line in csv.reader(humsavarTxt):
        code = re.match('[a-z](\d+)[a-z]', line[1], re.I)
        if code: 
            lookup[line[-2]].append(code.group(1))

print lookup['P04217']

Answer 1

Here’s a variant of the original code:

import csv, re
from collections import defaultdict

lookup = defaultdict(list)
with open('humsavar.txt', 'rb') as humsavarTxt:
    reader = csv.reader(humsavarTxt, delimiter=" ", skipinitialspace=True)
    for line in reader:
        code = re.search(r'(\d+)', line[3])
        lookup[line[1]].append(int(code.group(1)))

which produces

>>> lookup
defaultdict(<type 'list'>, {'P04217': [52, 395], 'Q9NRG9': [15]})
>>> lookup['P04217']
[52, 395]