Python csv Module
CSV is a very convenient file format when using EXCEL. Language like R
has very powerful functions reading and writing CSV files. In Python,
csv module provides read and write capability of tabular data in CSV format.
Suppose a file named "tp.csv" with following content:
Gene observed1 expected1 observed2 expected2
TTN 27 33 60 54
GATA3 38 20 17 35
HLA-DRB6 18 15 24 27
MUC16 13 15 28 26
NR1H2 11 15 29 25
GPRIN2 12 14 27 25
MAP3K1 15 14 24 25
GPRIN1 13 14 25 24
MLL3 12 14 26 24
MAP3K4 8 14 29 23
CDH1 17 12 17 22
ENSG00000245549 15 12 18 21
ZNF384 12 12 20 20
FRG1B 11 11 20 20
AKD1 9 11 21 19
OBSCN 12 11 17 18
NCOA3 8 10 20 18
USH2A 8 10 20 18
ENSG00000198786 12 10 15 17
Python script file "test.py" to read the file:
#!C:\python\python.exe
import csv
with open("tp.csv","r") as rad:
lines = csv.reader(rad, delimiter='\t')
for row in lines:
print (' -- '.join(row))
C:\> test.py
Gene -- observed1 -- expected1 -- observed2 -- expected2
TTN -- 27 -- 33 -- 60 -- 54
GATA3 -- 38 -- 20 -- 17 -- 35
HLA-DRB6 -- 18 -- 15 -- 24 -- 27
MUC16 -- 13 -- 15 -- 28 -- 26
NR1H2 -- 11 -- 15 -- 29 -- 25
GPRIN2 -- 12 -- 14 -- 27 -- 25
MAP3K1 -- 15 -- 14 -- 24 -- 25
GPRIN1 -- 13 -- 14 -- 25 -- 24
MLL3 -- 12 -- 14 -- 26 -- 24
MAP3K4 -- 8 -- 14 -- 29 -- 23
CDH1 -- 17 -- 12 -- 17 -- 22
ENSG00000245549 -- 15 -- 12 -- 18 -- 21
ZNF384 -- 12 -- 12 -- 20 -- 20
FRG1B -- 11 -- 11 -- 20 -- 20
AKD1 -- 9 -- 11 -- 21 -- 19
OBSCN -- 12 -- 11 -- 17 -- 18
NCOA3 -- 8 -- 10 -- 20 -- 18
USH2A -- 8 -- 10 -- 20 -- 18
ENSG00000198786 -- 12 -- 10 -- 15 -- 17
csv.writer object write data into a CSV file:
#!C:\python\python.exe
import csv
with open("tp.csv","w") as writfile:
writ = csv.writer(writfile, delimiter=',')
writ.writerow([1,2,3,4,5])
writ.writerow("python tutorial")
C:\> test.py
The content of file "tp.csv":
1,2,3,4,5
p,y,t,h,o,n, ,t,u,t,o,r,i,a,l
