Error

[arpit20328]

(base) arpit@jarvis:~/orignal_data/FRAGLE-main$ python main.py --input /home/arpit/orignal_data/FRAGLE-main/INPUT --output /home/arpit/orignal_data/FRAGLE-main/output_fragle/ --mode R --genome_build hg38
File "feature_generation.py", line 26
bamfile = f'{input_folder}/{file_}'
^
SyntaxError: invalid syntax
File "predict.py", line 138
print(f'WARNING: too few reads in sample {sample_names[i]}')
^
SyntaxError: invalid syntax

[lorisipsum]

Were you able to figure out a solution to this issue? I am also encountering it.

[arpit20328]

no

[Rafeed-bot]

You need to upgrade your python to 3.7 or above. The version you are using does not support python f-string. It is best if you install Fragle following the instructions given in GitHub; then you won't have trouble with version

[lorisipsum]

It appears that I am using a python version > 3.7. I followed the instructions given in GitHub, any suggestions on what may be happening?

/Pipelines/FRAGLE$ source ./Fragle/bin/activate
(Fragle) loris:/Pipelines/FRAGLE$ python
Python 3.8.15 (default, Nov 24 2022, 15:19:38)
[GCC 11.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.

[lorisipsum]

I should add that the pipeline worked on my actual data but not on the test data provided.

[Rafeed-bot]

bamfile = f'{input_folder}/{file_}'

The above line is the one giving error. Can you try and run this single line only using your test data? Basically, provide the input folder path in your input_folder variable and bam file name (say, test.bam) in your file_ variable. Then try and run:
bamfile = f'{input_folder}/{file_}'

There maybe certain type of string in your folder path or bam name which is causing the problem.