Compute inversion activity from pre-computed inversions

[meren]

This PR adds a new flag to the program anvi-report-inversions, --pre-computed-inversions, which takes in a previously reported inversions file, and calculates their activity. The help menu explains it:

CALCULATE ACTIVITY FROM KNOWN INVERSIONS?
  This input option is ONLY relevant to those who have already run the
  entire workflow and have their consensus inversions (i.e., 'CONSENSUS-
  INVERSIONS.txt') or sample-specific inversions (i.e., 'INVERSIONS-
  IN-[SAMPLE-NAME].txt') calculated. This input option will use the existing
  inversions reported in the input file and recalculate the inversion
  activity output. It is a great way to calculate inversions or refine them
  from a smaller set of genomes / metagenomes, and scale up the
  characterizations of their activity to thousands of metagenomes quickly
  (*cough* cheater *cough*). Please note that if you use this flag, most
  other options EXCEPT those that are listed below 'KEY ALGORITHMIC
  COMPONENT 04: COMPUTING INVERSION ACTIVITY' will be irrelevant, so you can
  skip all and take a look at the parameters there.

  --pre-computed-inversions INVERSIONS-FILE
                        A TAB-delimited file that lists sample-specific or
                        consensus inversions identified by the program `anvi-
                        report-inversions`. (default: None)

The PR does NOT include an update to the help docs for the program, but we need to update the section "Computing inversion activity".

[meren]

Well? DID IT WORK? ARE WE SAVED?

[FlorianTrigodet]

I want to try it with real world data, but I have issue with metagenomes that were recently deleted from the server WINK WINK

I need to clean some space and get these metagenomes before I can give you a final answer :D

[meren]

I'm not sure what you're talking abuut.

[FlorianTrigodet]

Tested, approved and very appreciated! 🍾