Eggnog-mapper

* Version 5.0.2 of the eggnog.db sqlite DB.
* <code>--resume</code> currently resumes most eggNOG-mapper stages: HMMER searches, seed orthologs from search hits, annotation, PFAM realignment, orthologs report, and creation of GFF with <code>--decorate_gff yes</code>. Diamond searches and MMseqs2 searches are atomic though, and GFF file decoration with <code>--decorate_gff FILE</code> will override the previous file if it exists.
* NCBI-based taxa DB is loaded into memory.
* eggNOG-mapper runs now as a pipeline of generators, which should allow annotating more records in a single run without memory issues related to this, except when creating GFF (<code>--decorate_gff yes/FILE</code>) or when realigning to PFAM (<code>--pfam_realign realign/denovo</code>).
* <code>--tax_scope_mode</code> option added, as a second layer of taxonomic scope control. <code>--tax_scope narrowest</code> option removed; <code>--tax_scope none</code> option added.
* <code>--tax_scope</code> (and <code>--tax_scope_mode</code>) can now read user-defined and also pre-defined files.
* The <code>--pfam_transfer</code> options were removed in favor of centralizing everything around <code>--tax_scope</code>
* <code>--decorate_gff_field</code> option added to control the GFF field used to link with annotations, and therefore to annotate GFF records. Now, <code>--decorate_gff FILE</code> does not accept the format <code>FILE:FIELD</code>.
* Bug fixes, minor changes.

* Added GFF decoration (<code>--decorate_gff</code> option), to create/modify a GFF including emapper hits and/or annotations.
* Output file comments start with "", making easier filtering them without removing the header (which starts with "")
* Fixed seed_orthologs header.
* Fixed <code>pident</code> not shown in seed_orthologs output.

- Added --trans_table (Diamond's --query-gencode, MMseqs2's --translation-table, Prodigal's -g/--trans-table) option, to specify a translation table for gene prediction and blastx searches.
- Added --training_genome and --training_file options, to run Prodigal training mode.
- Default search thresholds (pident, score, query and subject coverage) are set to None.
- Both Diamond and MMseqs2 seed_orthologs file includes now percentage identity (pident), position of hits (qstart, qend, sstart, send) and query coverage (qcov) and subject coverage (scov).
- Added --outfmt_short option for Diamond, to run it producing only query, subject, evalue and score as output. This option could be useful to obtain better performance when no thresholds for pident, and query and subject coverages are used (see Diamond docs about traceback). Of course, seed_orthologs file will contain only those 4 fields.
- Added subject coverage (target_coverage) to gff output from blastx based gene predictions.
- Added --block_size (Diamond's -b/--block-size) and --index_chunks (Diamond's -c/--index-chunks) options.
Bug fixes.

* Fix 275 , default data directory for download_eggnog_data.py
* Added script create_db.py to create diamond/mmseqs databases for the user-specified list of taxa

This is the first release for the merge of the refactor version into master.

* All code migrated to Python 3. Therefore, python3 is now required to run eggnog-mapper scripts.
* HMMER search capabilities moved to new scripts: '''''hmm_search.py''''', '''''hmm_server.py''''', '''''hmm_worker.py'''''.
* Changes in output format, specially the "annotations" output file.
* Changes in available parameters and behaviour of existing ones.
* Added some integration and unit tests
* New ''--tax_scope'' modes.
* Added eggNOG DB version to ''-v, --version'' options.
* New eggnog DB version 5.0.1 including PFAM annotations and PFAM HMMs.
* Added expected eggNOG DB version, and warning if found version is different than expected one.
* Added PFAM annotations, which are directly transferred from orthologs.
* Added ''--pfam transfer'' option to ''emapper.py''.
* Gene prediction step using Prodigal.
* Search and annotation of ORFs using diamond blastx or MMseqs2. This can be used to annotate ORFs of contigs without using Prodigal.
* MMseqs2 support for the search step of eggNOG-mapper.
* Parameters to allow users to control sensitivity of diamond/MMseqs2 searches.
* Improved report of orthologs.
* NCBITaxa support is now included in eggNOG-mapper without relying on ete3.
* ''--md5'' option, which can be used to add the md5 hash of the query as a new column in the annotations output file.
* ''-m cache'' mode and ''-c FILE'' options, to annotate using an annotations file with md5 hashes as cached results. A fasta file with unannotated sequences is output also, which can be used in a subsequent conventional emapper annotation run.
* "Bottom-top" orthology search if no proper orthologs are retrieved from a priori chosen best OG.
* ''--go_evidence all'' option to report all GO terms.
* ''--dbmem'' option to pre-load the ''eggnog.db'' sqlite3 DB into memory.
* if `--translate` option is used (along with `--itype CDS`), input sequences will be translated to proteins before searching with either diamond "blastp", mmseqs "blastp" or hmmer. If `--itype CDS` is used without `--translate`, it will raise error for hmmer, but it will run diamond or mmseqs in "blastx" modes.
* Bug fix when running hmmer with only-numerical identifiers in input sequences
* Other minor changes

- Corrects version number reported when `emapper.py` is executed