Bug: NameError: name 'BedGraphIO' is not defined. Did you mean: 'bedGraphIO'?

[acv21]

Hello,

I am using MACS3 v. 3.0.2 with Python v. 3.9.20 and Numpy v. 2.0.2. I tried running the following code from the folder containing my .bam files:

for i in ./*.bam; do 
 macs3 hmmratac -i $i -n ${i%.bam} --outdir ./out -u 20 -l 10 -c 1.2 --save-digested --save-states --save-likelihoods -e /dir/mm10-blacklist.v2.bed
done

I get the following error message for each sample:

Traceback (most recent call last):
File "/package/python-cbrg/current/3.11/bin/macs3", line 983, in
main()
File "/package/python-cbrg/current/3.11/bin/macs3", line 97, in main
run( args )
File "/package/python-cbrg/current/3.11/lib/python3.11/site-packages/MACS3/Commands/hmmratac_cmd.py", line 168, in run
bdgshort = BedGraphIO( short_bdgfile, data = digested_atac_signals[ 0 ] )
^^^^^^^^^^
NameError: name 'BedGraphIO' is not defined. Did you mean: 'bedGraphIO'?

I think this may have been fixed on main branch (8b4fbe0#diff-12485f39398e04990a47b92449150ec60f8a87fdf2cbadbbc58bb3869c57a471R34). Is there anything I can do to be able to run the analysis before the next MACS3 version is released, with the fix for this bug?

Thank you!

[philippadoherty]

Hi @acv21, thanks for spotting that bug!
You can follow these instructions for installing from source via pip. The default should be to install from the master branch.

Please let us know if you have any issues with that.

Thanks!