Bug fix and new features

apcamargo commented 4 years ago

I know that opening a PR with multiple unrelated fixes and new functions isn't ideal, but I've been working with this slightly modified version of enrichM and I decided to share my fixes and additions.

This PR does the following:

Fixes https://github.com/geronimp/enrichM/issues/105
Fixes https://github.com/geronimp/enrichM/issues/104
Fixes https://github.com/geronimp/enrichM/issues/103
Splits Pfam and TIGRFAM HMM cutoffs into separate arguments. This way the user can use, for instance, --cut_ga for Pfam and --cut_nc for TIGRFAM.
If two Pfam domains overlap the one with the highest E-value is discarded if both belong to the same clan. This behaviour is the same of pfam_scan.pl.

geronimp commented 3 years ago

Hey,

I really appreciate these additions, thanks for those bug fixes. I've just merged them in (some time later).

apcamargo commented 3 years ago

Thanks, @geronimp!

Another think that I did was to update all the databases (and their respetive pickles) to their latest versions. If you are interested, I can make those files available to you.

geronimp / enrichM

Bug fix and new features #107