from pyfasta import Fasta

[YayanFeng55]

Dear Zoes,

Thanks for developing this software. I have tested the pipelines you suggested. But for the first step:

1. python main.py -h
   It occured below error:

Traceback (most recent call last):
File "main.py", line 7, in
from utils import DataGenerator, MutGenerator, GetSummaryStatisticsCallback, writeFile
File "/hdd/fengy2/Softwares/MtBNN/utils.py", line 8, in
from pyfasta import Fasta
File "/home0/fengy2/miniconda3/envs/MtBNN/lib/python3.8/site-packages/pyfasta/init.py", line 3, in
from fasta import Fasta, complement, DuplicateHeaderException
ImportError: cannot import name 'Fasta' from 'fasta' (/home0/fengy2/miniconda3/envs/MtBNN/lib/python3.8/site-packages/fasta/init.py)

I solved this issue by changing 'from pyfasta import Fasta' to 'from pyfaidx import Fasta'.

2. Then I run bash script/preparejsonfile.sh. It occured below error:

2023-06-11 15:44:07.848 | INFO | main:main:102 - start handling gm12878_dsqtl.csv
Traceback (most recent call last):
File "/home0/fengy2/miniconda3/envs/MtBNN/lib/python3.8/runpy.py", line 192, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/home0/fengy2/miniconda3/envs/MtBNN/lib/python3.8/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/hdd/fengy2/Softwares/MtBNN/Tools/narrow2json.py", line 156, in
main(Lfile, path, mutfiles)
File "/hdd/fengy2/Softwares/MtBNN/Tools/narrow2json.py", line 104, in main
data=load_mut(p)
File "/hdd/fengy2/Softwares/MtBNN/Tools/narrow2json.py", line 89, in load_mut
assert Genome[c][int(p)-1].upper()==name[-2].upper()
AttributeError: 'Sequence' object has no attribute 'upper'

Do you have any ideas how to solve this issue? Does this issue have any correlations with my changes ('from pyfasta import Fasta' to 'from pyfaidx import Fasta')

Thanks
Yayan