Shiny Mantis 1.1.1

fix pfam metadata

Former-commit-id: b0be50a39bfceee6211e203d6571950707fd9369

Shiny Mantis

Added Diamond support, the user can now add sequences and use those as reference. Mantis now has HMMER and Diamond integration, hits coming from either homology search tool are used.

Added CDS translation of RNA and DNA to protein sequences. The user can provide a genetic code (default 11) when running Mantis with -gc

Added reference weight for heuristic and bpo algorithms (previously only dfs supported this)

Added a transporter reference database (TCDB)

Added cores variable to setup_databases

Added kill_switch instead of using Exceptions (clearer traceback)

Changed output and variables nomenclature to be more agnostic (HMM -> reference)

release resubmission

Added new NPFM for taxa-specific annotation
general TSHMMs now come from top NCBI taxon IDs
user can now choose which eggNOG TSHMM to use, rather than downloading whole eggNOG database
added kegg matrix output
added more execution options
updated wiki
general bug fixing and other minor improvements

v1.01

added pfam2go
split nogsql into smaller files to not have issues with git lfs
other minor improvements in stability

Mantis version 1.0

Release v1.0, accompanied by pre-print at https://doi.org/10.1101/2020.11.02.360933