small part of my csv
file is like the following lines:
481116 ABCF3 466 0 ENSG00000161204 0
485921 ABCF3 466 0 ENSG00000161204 0
489719 ABCF3 466 0 ENSG00000161204 0
498136 ABCF3 466 2 ENSG00000161204 0.0019723866
273359 ABHD10 326 78 ENSG00000144827 0.0301158301
491580 ABHD10 326 0 ENSG00000144827 0
493784 ABHD10 326 0 ENSG00000144827 0
494817 ABHD10 326 1 ENSG00000144827 0.0012484395
the columns are separated by ","
in the file. in the 2nd column there are many repeated ids and I would like to select only one of the ids based the values in the 6th column. in other word, for each id I want to choose the one with the highest number in the column 6. the results for the mentioned part, must be like this.
498136 ABCF3 466 2 ENSG00000161204 0.0019723866
273359 ABHD10 326 78 ENSG00000144827 0.0301158301
I have tried to make it in python and wrote some pieces of codes in the following framework but non of them worked:
with open('data.csv') as f, open('out.txt', 'w') as out:
line = [line.split(',')for line in f]
.
.
out.write(','.join(results))
you_data.csv:
481116,ABCF3, 466,0, ENSG00000161204,0
485921,ABCF3, 466,0, ENSG00000161204,0
489719,ABCF3, 466,0, ENSG00000161204,0
498136,ABCF3, 466,2, ENSG00000161204,0.0019723866
273359,ABHD10,326,78,ENSG00000144827,0.0301158301
491580,ABHD10,326,0, ENSG00000144827,0
493784,ABHD10,326,0, ENSG00000144827,0
494817,ABHD10,326,1, ENSG00000144827,0.0012484395
code:
import csv
from collections import defaultdict
with open('you_data.csv', newline='') as f, open('out.csv', 'w', newline='') as out:
f_reader = csv.reader(f)
out_writer = csv.writer(out)
d = defaultdict(list)
for line in f_reader:
d[line[1]].append(line)
for _,v in d.items():
new_line = sorted(v, key=lambda i:float(i[5]), reverse=True)[0]
out_writer.writerow(new_line)
out.csv:
498136,ABCF3, 466,2, ENSG00000161204,0.0019723866
273359,ABHD10,326,78,ENSG00000144827,0.0301158301
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