Where is sample_to_markers.py?

Hi, thanks for developing this excellent tool!

I’ve been studying strainphlan2 example from

but when I run step2, I can’t find this sample_to_markers.py file

$ python sample_to_markers.py -i sams/*.sam.bz2 -o consensus_markers

would you please tell me where can I download this file ???

I also can’t find strainphlan2.py

Hi, thanks for getting in contact.
StrainPhlAn2 was an intermediate version that now is not longer available. If you are using the conda version of metaphlan 3.0, you can take a look on this tutorial: https://github.com/biobakery/MetaPhlAn/wiki/StrainPhlAn-3.0
In a short, a similar tutorial to the one you are pointing will be available too