CODEWITHSUNDEEP
pythonregex
upendra
upendra

Reputation: 2189

how to parse a file and write to an output file in python

i am newbie to python. I am trying to parse a file to extract certain columns and write to an output file. I was able to parse and extract the desired columns but having trouble writing them to an output file.

Here is the original test file:

EGW05759        Pld5    I79_005987      GO_function: GO:0003824 - catalytic activity [Evidence IEA]; GO_process: GO:0008152 - metabolic process [Evidence IEA]                                  
EGW05760        Exo1    I79_005988      GO_function: GO:0003677 - DNA binding [Evidence IEA]; GO_function: GO:0003824 - catalytic activity [Evidence IEA]; GO_function: GO:0004518 - nuclease activity [Evidence IEA]; GO_process: GO:0006281 - DNA repair [Evidence IEA]

Here is my python code

f = open('test_parsing.txt', 'rU')
f1 = open('test_parsing_out.txt', 'a')
for line in f:
   match = re.search('\w+\s+(\w+)\s+\w+\s+\w+\:', line)
   match1 = re.findall('GO:\d+', line)
   f1.write(match.group(1), match1)
f1.close()

Basically i want the output to look like this (though i know my code is not complete to achieve this)

Pld5 GO:0003824:GO:0008152
Exo1 GO:0003677:GO:0003824:GO:0004518:GO:0006281

Thanks

Upendra

Upvotes: 0

Views: 1383

Answers (2)

Hasan Ramezani
Hasan Ramezani

Reputation: 5194

f = open('test_parsing.txt', 'rU')
f1 = open('test_parsing_out.txt', 'a')
for line in f:
    match = re.search('\w+\s+(\w+)\s+\w+\s+\w+\:', line)
    match1 = re.findall('GO:\d+', line)
    f1.write('%s %s \n'%(match.group(1), ''.join(match1)))
f1.close()

Upvotes: 4

Adam Smith
Adam Smith

Reputation: 54213

Using the csv module:

import csv, re

with open('test_parsing.txt', 'rU') as infile, open('test_parsing_out.txt', 'a') as outfile:
    reader = csv.reader(infile, delimiter="\t")
    for line in reader:
        result = line[1] + " " + ':'.join(re.findall("GO:\d{6}", line[3]))
        outfile.write(result + "\n")

# OUTPUT
Pld5 GO:000382:GO:000815
Exo1 GO:000367:GO:000382:GO:000451:GO:000628

Upvotes: 2

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