get_bad_or_unmapped_hq.py

[NahlaHu]

Hi,

I was trying to run the command python <path_to_Cogent>/get_bad_or_unmapped_hq.py hq.fasta hq.5merge
and I have this error:
File "/usr/local/Cogent/Cogent/helper_scripts/get_bad_or_unmapped_hq.py", line 20, in
print >> sys.stderr, "Reading transcript file {0}....".format(input)
TypeError: unsupported operand type(s) for >>: 'builtin_function_or_method' and '_io.TextIOWrapper'. Did you mean "print(, file=<output_stream>)"?

Thanks

[Magdoll]

HI @NahlaHu - my guess is you are not using Python 3?
-Liz

[NahlaHu]

Thanks Liz,
Well, the python version we have is Python 3.8.13.
And the badmapped.fasta file was generated, but sized zero and generate this error. what is your suggestion?
Thanks

[JohnnyChen1113]

Thanks Liz, Well, the python version we have is Python 3.8.13. And the badmapped.fasta file was generated, but sized zero and generate this error. what is your suggestion? Thanks

The get_bad_or_unmapped_hq.py script written by python 2， so when you change your python version to python 2，that will generate the result smoothly.