Do you want to merge multiple profile HMMs into one?
input_fasta_filenames = ["/path/to/fasta/file/with/all/gap/columns/removed", "/path/to/another/fasta/file/with/all/gap/columns/removed"]
backbone_alignment = "/path/to/backbone/alignment"
mapping = create_mappings_helper(input_fasta_filenames, backbone_alignment)
Mapping will be a map of input fasta filename indices to a secondary map
The secondary map is a mapping of column index in the backbone alignment to the corresponding column index in the input fasta filename
For some example input files and expected outputs, look at the test directories and the test file
- biopython
- click
- pyhmmer-sepp
- pytest
git clone https://github.com/MinhyukPark/HMMerge.git
cd HMMerge
pytest test.py