The script to generate kmers does not work on python3. Possible infinite loop in find_kmers
mahmudhera opened this issue · 2 comments
mahmudhera commented
The error message is as follows:
Traceback (most recent call last):
File "kmer_generator.py", line 127, in
if len(record) < args.min_chr_length:
TypeError: '<' not supported between instances of 'int' and 'str'.
There is also a possible infinite loop in find_kmers function. This happens when the index is less than 20. For example, when index=19, forward=True and end=True, the position is negative, and the loop hits continue, and loops forever.
schmidt73 commented
Thanks for the bug report. I'll work on this presently.
schmidt73 commented
Both issues have been fixed. The former was caused because I forgot to enforce the type of the arguments to int
. The latter was fixed by ensuring that index is incremented on every iteration of the loop.