How to copy specific data out of a file using python?

Question

I have some large data files and I want to copy out certain pieces of data on each line, basically an ID code. The ID code has a | on one side and a space on the other. I was wondering would it be possible to pull out just the ID. Also I have two data files, one has 4 ID codes per line and the other has 23 per line.

At the moment I'm thinking something like copying each line from the data file, then subtract the strings from each other to get the desired ID code, but surely there must be an easier way! Help?

Here is an example of a line from the data file that I'm working with

cluster8032:  WoodR1|Wood_4286 Q8R1|EIK58010 F113|AEV64487.1 NFM421|PSEBR_a4327

and from this line I would want to output on separate lines

Wood_4286
EIK58010
AEV644870.1
PSEBR_a4327

Answer 1

Use the regex module for such a task. The following code shows you how to extract the ID's from a string (works for any number of ID's as long as they are structured the same way).

import re
s = """cluster8032:  WoodR1|Wood_4286 Q8R1|EIK58010 F113|AEV64487.1 NFM421|PSEBR_a4327"""
results = re.findall('\|([^ ]*)',s) #list of ids that have been extracted from string
print('\n'.join(results)) #pretty output

Output:

Wood_4286
EIK58010
AEV64487.1
PSEBR_a4327

To write the output to a file:

with open('out.txt', mode = 'w') as filehandle:
    filehandle.write('\n'.join(results))

For more information, see the regex module documentation.

Answer 2

If all your lines have the given format, a simple split is enough:

#split by '|' and the result by space
ids = [x.split()[0] for x in line.split("|")[1:]]