Error in passing arguments

Question

import sys
import argparse
import ORFALGO as orf
#get filenames from command line arguments
firstSeq = sys.argv[1]
if len(sys.argv)>=3:
    resultFile = sys.argv[2]
else:
    resultFile='ORF.txt'
def parse_fasta(fasta): 
        sequences=''
        sep=''
        with open(fasta) as f:
            next(f)
            for line in f:
                sequences += (line.strip())
        return sequences
seq= parse_fasta(firstSeq)

File "C:\Users\ram\Desktop\python\hw2\ass2\LongORF.py", line 6, in <module>
    firstSeq = sys.argv[1]
IndexError: list index out of range

And how are you calling your script? – Tim Oct 22 '14 at 16:59 — Tim, Oct 22 '14 at 16:59
Are you passing a file name to the script when you run it? – Bill the Lizard Oct 22 '14 at 17:01 — Bill the Lizard, Oct 22 '14 at 17:01

score 0 · Answer 1 · answered Oct 22 '14 at 16:59

0

sys.argv[0] is your script name, you should provide at least a parameter when invoking your script. Currently sys.argv does not have a index=1 element thus error occurs.

answered Oct 22 '14 at 16:59

laike9m

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score 0 · Answer 2 · answered Oct 22 '14 at 17:00

0

You need to run it as

python LongORF.py firstSeq resultFile

Here

LongORF.py is sys.argv[0] firstSeq is sys.argv[1] resultFile is sys.argv[2]

answered Oct 22 '14 at 17:00

Rishi Dua

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Error in passing arguments

2 Answers2