Disturbing code with the hhsearch and hmmsearch wrappers

[abdulle-sabaf]

Just cloned the project and was giving a try of inference and I ran into this:

Traceback (most recent call last):
  File "inference.py", line 658, in <module>
    main(args)
  File "inference.py", line 535, in main
    alignment_runner.run(chain_fasta_path, local_alignment_dir)
  File "/xTrimoMultimer/xtrimomultimer/data/data_pipeline.py", line 476, in run
    if self.template_searcher.input_format == "sto":
AttributeError: 'HHSearch' object has no attribute 'input_format'

So I took a look at this HHSearch object at data/tools/hhsearch.py. Turns out that it doesn't have a input_format property. So I tried to seek this property name within the package and found that it is provided in a certain Hmmsearch class. So it seems that these 2 wrappers are so alike that the HHSearch class should've had the same properties and methods but they were somehow forgotten.