Guess bit_cutoffs in hmmsearch

[jpjarnoux]

Hi Martin,

I'm trying to align multiple HMM to proteins; some of my HMM has a GA score, and others do not.

Is there a way to leave hmmsearch to guess if he must use the bit_cutoffs for this HMM? It would be great to have this possibility rather than make two batches of HMM. I would also leave the possibility of forcing the bit_cutoff as an option.
I know it's a little to do two batches, but the inside code of the pipeline is a little more complex, and as Pyhmmer reads the HMM to get the cutoff values, if the cutoff line begins with GA, we could save the gathering type of cutoff.

Let me know if you think it's a good idea and if you could add this or not in the future.

Thanks