Eggnog-mapper

- Changes in GFF decoration to (hopefully) fix issue 367 , in which positions were relative to the ORF (1-end) instead of relative to the contig which contains the ORF. Now, 2 GFF files will be created when using gene prediction and gff decoration: one ".genepred.gff" from either Prodigal or blastx-like hits, one ".decorated.gff" with the annotations added as attributes.
- Update the --resume procedure. Now, most files are created from scratch, being resumed the search (if a ".emapper.hits" exists) and annotations (if a ".emapper.hits" exists, or ".emapper.seed_orthologs" if using --annotate_hits_table option; and if a partial ".emapper.annotations" file exists).
- Now it should be possible to use Biopython 1.78 (python 3.9) which removed the BioAlphabet module.
- emapper.py's --temp_dir option is now linked to Diamond's --tmpdir option.
- Update / Bug fix (issue 328) regarding report of orthologs, where the seed ortholog was listed in every orthology category. Now the seed ortholog should be tagged as "seed" in the "orth_type" column.
- Help description and default values of parameters of emapper.py are now provided more consistently (PR 346 addressing issue 344, thanks nick-youngblut). Also done by nick-youngblut for all the other main scripts (PR 347).
- --version now reports the Diamond/MMseqs2 version found (either from PATH or from eggNOG-mapper bundled bin).
- Fixed a bug when transferring PFAM annotations from denovo hmmpgmd search and number of queries was large (>15000).

- Updated citation of eggNOG-mapper.
- Updated citation of Diamond.
- Diamond's `--iterate` mode is now used by default. To disabled it when running `emapper.py`, use `--dmnd_iterate no`.
- Added `--dmnd_ignore_warnings` option, to activate Diamond's `--ignore-warnings` option.
- Added `--dmnd_algo` option, to control Diamond's `--algo` option. It can be used to perform a much faster search with small input sets of sequences using `--dmnd_algo ctg`.
- Added `--mp_start_method` option, to control the Python's multprocessing start method. Only use it when the default is not working properly in your OS.
- Minor changes related with `hmmpgmd` searches.

* New Diamond version 2.0.11 bundled.
* Added new options for diamond mode (require using Diamond version 2.0.11): <code>--dmnd_iterate</code> (Diamond's <code>--iterate</code> option), <code>--sensmode fast</code>, and <code>--sensmode default</code>.
* Bug fix (issues 313 and 319), when parsing GFF files with "." in the "score" field.
* <code>--dmnd_frameshift INT</code> option to control Diamond's <code>--frameshift/-F</code> option.
* Bug fix / try to address the <code>main __spec__</code> bug (issue 299). For a fix in version 2.1.4, check pre-release [[https://github.com/eggnogdb/eggnog-mapper/releases/tag/2.1.4-main_spec]]
* Minor progress report text fix.

documentation: https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5

2.1.4-main_spec
This is a test release to check whether annotation can be run with multiprocessing and without issues related with __spec__ in __main__ (see issue 299

* <code>--excel</code> option to output annotations in .xlsx format.
* Recalibration of PFAM annotation from orthologs.

* Bug fix (issue 301), when running <code>--pfam_realign realign</code> and there are seeds without annotations.
* Bug fix (issue 303), when running <code>--pfam_realign denovo</code> and there are 100 queries or more (so that <code>hmmpgmd</code> servers are used).
* Other minor changes (issue 302)

* Orthologs retrieved bottom-up from narrowest OG to max annotation level OG.
* Changes in format of annotations and gff output files (check https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.2#Output_format).