Inconsistencies arising from input_file_regex

[wichne]

I had input files named 'protein_A.SEED.faa', and specified 'input_file_extx: ["faa"]' and 'input_file_regex: ".SEED.faa" in the config.yaml.
Building the models worked fine, but when I tried to search, snekmer was looking for scorer, model and kmers files that looked like "protein_A.ext", while the files that 'model' output looked like "protein_A.SEED.ext".
I made soft links of the existing files to the expected names, but the search process failed during the vectorize step (this is a separate issue, I think.)

So I went back and changed the input_file_regex back to the default ".*"
Again, model building ran fine, but when I tried to search, snekmer was expecting files that looked like "protein_A_SEED.ext" while the existing files looked like "protein_A.SEED.ext").