Release v1.2.4 8/3/2021

Potentially breaking change in this release for those parsing annotation.tsv results.
VOGDB hits columns have been renamed from vogdb_description and vogdb_categories to
vogdb_id (previously unreported), vodb_categories and vogdb_hit
(equivalent to vogdb_description).

Changelog

• Add anammox to distillate
• Fix more no hits bugs (thanks to @cerebis)
• VOGDB output columns renamed to match other databases
• Big upgrade to merge annotations, now includes all parts of DRAM annotate output
• Added option to run KOfam with dbCAN thresholds (used in other DRAM hmmscan applications) instead of KOfam recommended thresholds
• @rmFlynn fixed bug where VirSorter 2 headers were not recognized by DRAM-v
• @rmFlynn upgraded warnings and error messages for DRAM-v around parsing affi contigs and fasta files
• Fixed bug were non-cazy ID's were pulled out of dbCAN descriptions

v1.2.0

Change Log

• Handle when there are no significant kofamhits
• Fix DRAM genome stats to always give scaffold location even if grouping by other unit
• Fix last genome being skipped when number of genomes was > genomes per liquor
• Don't kill everything if bins aren't in gtdb or checkM, just give warning and fill
• Add ability for DRAM and DRAM-v to take custom distillate sheets
• Add flag to DRAM distill to give gene names and not counts in distillate
• Fix where making gbk file would fail if '>' included in fasta header
• Fix DRAM-v distill breaking at making viral stats with non VirSorter 1 viruses
• Add flag to DRAM distill to set the number of genomes per liquor
• Update default dbCAN2 version to v9
• Metabolism updates
  • Remove database identifiers from polyphenolic metabolism that were too loose
  • Add sugar metabolisms to distillate

August 19th release that is actually out on August 21st

New release for August 2019. Take note now sqlalchemy, barrnap and altair are not dependencies. All can be installed via conda.

After this release a new structure for branches is being used. Master branch will be the release + any bugfixes associated with getting the release to work. This branch should be stable. The dev branch holds all features added since the last release. This branch is semi-stable. This branch will be rolled into master at each new release. Individual features will be developed on their own branches. These are not at all stable. Once they are tested and working they can be rolled into dev.

Changelog:

• Add gene start, end and strandedness to annotations
• Add GTDBk taxonomy and checkM contamination and completeness to annotations
• Add --skip_trnascan flag
• Work around is to set $TMPDIR variable
• Add ability to use custom fasta as annotation databases (BLAST style search only (at this point))
• All fasta headers now stored in sqlite db
• Output genbank file per bin with annotation information
• Add rRNA detection using barrnap
• Creation of genome_stats.tsv
• Creation of funcation_heatmap.html
• Bugfixes surrounding processing of small genomes with few annotations
• Various bugfixes

Release to be rolled out to OSU and CSU for testing

Make an actually useful README.md

It's pycharm's markdown so it might need to be fixed for github.