I am trying to use csv.reader() to pull values from a database for later comparison. I want to have the reader index the row so that each element in the list corresponds to a comma separated value, instead of the character in the row.
My code:
with open(sys.argv[1]) as str_db:
str_reader = csv.reader(str_db)
line_count = 0
fields = []
for row in str_db:
if line_count == 0:
fields = re.split(",", row)
line_count += 1
else:
print(f"{fields[0]}: {row[0]}, {fields[1]}: {row[1]}, {fields[2]}: {row[2]}, {fields[3]}: {row[3]}")
Pulling from the file = argv[1]:
name,AGATC,AATG,TATC
Alice,2,8,3
Bob,4,1,5
Charlie,3,2,5
Where I expect to see:
name: Alice, AGATC: 2, AATG: 8, TATC: 3
name: Bob, AGATC: 4, AATG: 1, TATC: 5
name: Charlie, AGATC: 3, AATG: 2, TATC: 5
Instead this is my output:
name: A, AGATC: l, AATG: i, TATC
: c
name: B, AGATC: o, AATG: b, TATC
: ,
name: C, AGATC: h, AATG: a, TATC
: r
Bonus thanks if you can tell me why a new line starts at the end of TATC.
I've tried:
with open(sys.argv[1]) as str_db:
str_reader = csv.reader(str_db, delimiter = ',')
line_count = 0
fields = []
for row in str_db:
if line_count == 0:
fields = re.split(",", row)
line_count += 1
else:
print(f"{fields[0]}: {row[0]}, {fields[1]}: {row[1]}, {fields[2]}: {row[2]}, {fields[3]}: {row[3]}")
but there is no change.
Actually using the reader produces the correct results. Note newline=''
is recommended for opening files with csv.reader
and csv.writer
:
import csv
with open('input.csv',newline='') as str_db:
reader = csv.reader(str_db)
fields = next(reader)
for row in reader:
print(f"{fields[0]}: {row[0]}, {fields[1]}: {row[1]}, {fields[2]}: {row[2]}, {fields[3]}: {row[3]}")
Output:
name: Alice, AGATC: 2, AATG: 8, TATC: 3
name: Bob, AGATC: 4, AATG: 1, TATC: 5
name: Charlie, AGATC: 3, AATG: 2, TATC: 5
DictReader
can help a little:
import csv
with open('input.csv') as str_db:
reader = csv.DictReader(str_db)
for row in reader:
print(', '.join([f'{key}: {value}' for key,value in row.items()]))
(same output)