CodFreq allow entry point from .sam file

[TKMarkCheng]

Thank you for this wonderful pipeline.

Is it possible to add in the functionality to allow for entering in processed .bam file (adapter trimmed, aligned, primer trimmed) instead of fastqs?

I wanted to experiment with different pre-processing methods.

[gpcr]

python3 /path_to_codfreq/scripts>/sam2codfreq.py
-r /path_to_your_profile>/HIV1.json
-o /path_to_output_codfreq_file_name..json
/path_to_HIV1_aligned_bam_file.bam

[TKMarkCheng]

I initially thought the same, but codfreq/scripts/sam2codfreq.py does not allow the input of a profile.

usage: codfreq/scripts/sam2codfreq.py <SAMFILE> <OUTPUT>

I've noticed codfreq/codfreq/sam2codfreq.py does but is more complex and is not a terminal callable script (as it does not have)

if __name__ == '__main__':
  main()

[philiptzou]

Yeah it’s currently not an exposed feature. However I believe you can create a main script, then import and expose the function from sam2codfreq to achieve what you want.

…

On Tue, May 6, 2025 at 9:30 AM Mark Cheng ***@***.***> wrote: *TKMarkCheng* left a comment (hivdb/codfreq#10) <#10 (comment)> I initially thought the same, but codfreq/*scripts*/sam2codfreq.py <https://github.com/hivdb/codfreq/blob/main/scripts/sam2codfreq.py> does not allow the input of a profile. usage: codfreq/scripts/sam2codfreq.py <SAMFILE> <OUTPUT> I've noticed codfreq/*codfreq*/sam2codfreq.py <https://github.com/hivdb/codfreq/blob/main/codfreq/sam2codfreq.py> does but is more complex and is not a terminal callable script (as it does not have) if __name__ == '__main__': main() — Reply to this email directly, view it on GitHub <#10 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGFXCM3H6CQYVQ2SZX7QDD25DPRBAVCNFSM6AAAAABQT2XZKCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDQNJVGIYTMNZYGE> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>