I’ve got a program to find DNA matches. We’ve been given a one line text file for finding the longest sequence of STR(Short Tandem Repeats) then match the result with a database which has been a .cvs file as below:
> name,AGATC,TTTTTTCT,AATG,TCTAG,GATA,TATC,GAAA,TCTG > Albus,15,49,38,5,14,44,14,12 > Draco,9,13,8,26,15,25,41,39 > Ginny,37,47,10,23,5,48,28,23 > Harry,46,49,48,29,15,5,28,40
After getting results for longest sequence amounts(as integer) I’m trying to find a match in this cvs file and print the value in the first column (name) when I found the matching numbers of STR. I’m checking the program with
print() and it prints ‘no match’ until the matched name then stops with below error code:
Traceback (most recent call last): File "dna.py", line 37, in <module> main() File "dna.py", line 27, in main print(row) KeyError: 0
My program probably finds the match but can’t print out than exits. Could you please help me? TIA
def main(): for i in SEQ.keys(): SEQ[i] = find_longest_sequence(i) print(SEQ.items()) with open(sys.argv,'r') as f: db = csv.DictReader(f) for row in db: if int(row['AGATC']) == SEQ['AGATC'] and int(row['AATG']) == SEQ['AATG'] and int(row['TATC']) == SEQ['TATC']: print(row) else: print("No match")
I used the data you provided and made a test.csv
name,AGATC,TTTTTTCT,AATG,TCTAG,GATA,TATC,GAAA,TCTG Albus,15,49,38,5,14,44,14,12 Draco,9,13,8,26,15,25,41,39 Ginny,37,47,10,23,5,48,28,23 Harry,46,49,48,29,15,5,28,40
Then tested with the folowing code (py csv-test.py test.csv):
import csv import sys with open(sys.argv, "r") as f: db = csv.DictReader(f) for row in db: if int(row['AGATC']) == 15: print(row['name'])
And the result was “Albus”.
I get the same KeyError as you do.
Do I miss something?