Mismatch: PRScsx.py logic does not support multi-population input as described in README

[KrysT4L75]

Dear Author,

I am writing to report a severe discrepancy between the documentation (README.md) and the actual source code (PRScsx.py) provided in this repository.

The Issue: The README clearly instructs users to input multiple populations (e.g., --pop=EUR,EAS) and multiple summary statistic files. However, the PRScsx.py script in the repository appears to contain single-population logic (likely from the original PRS-CS), which fails to loop through multiple populations or read the corresponding reference panels.

Evidence:

README Instruction: The README explicitly states:

python PRScsx.py ... --pop=EUR,EAS ...

Code Logic (Current Version): Upon inspecting the source code after encountering multiple UnboundLocalError and IndexError crashes, I found that the main() function rigidly looks for a single reference file (e.g., snpinfo_mult_1kg_hm3) and lacks the necessary loop (for pp in range(n_pop)) to handle multiple populations.

Request: Could you please verify if the wrong version of PRScsx.py was accidentally pushed to the master branch? Please update the repository with the correct cross-population compatible script as soon as possible.

Best regards,
kryst4l

[getian107]

snpinfo_mult_1kg_hm3 is a file that contains information from all populations.

The algorithm then iterates through multiple populations, see e.g., line 78 in mcmc_gtb.py.

If you encounter any error when running the software, could you post the error message and the commend line you used to call the program?