v3.3.2 Cenote-Taker 3: Large Cenotoid Earthlings

Updates:

1. version change from 3.3.1 to 3.3.2
2. using shutil.which instead of find_executable to check for external dependencies
3. python dependency check for pyrodigal-gv allows for packages called either pyrodigal-gv or pyrodigal_gv (this changed between 0.3.1 and 0.3.2 of that tool) #15
4. Changing "Chunk" suffix from @Chunk_# to @C# to shorten virus names. This helps with loading .gbf files into Geneious #13

What's Changed

• to v3.3.2, Update5 by @mtisza1 in #17

Full Changelog: v3.3.1...v3.3.2

v3.3.1 Cenote-Taker 3: Majestic Gull Attack

Changes from v3.3.0:

1. Added argument --max_dtr_assess. Users can enter a maximum contig length to evaluate DTRs (default 1000000). Practically, long DTR-containing contigs are probably bacterial chromosomes and should be evaluated for prophages and pruned. Since DTR-containing contigs do not get pruned, this was preventing some bacterial chromosome assemblies from getting pruning treatment. #6
2. Fixed hhpred_to_table.py gene_name variable parsing, which previously incorrectly used .strip() function.
3. Fixed location of MMSEQS_outdir in get_ct3_dbs command to avoid error.
4. For read-mapping, --seqtech now effects minimap2 settings

What's Changed

• Update4, to v3.3.1 by @mtisza1 in #7

Full Changelog: v3.3.0...v3.3.1

v3.3.0 Cenote-Taker 3: Sauceman's grotto

Changes from v3.2.1:

1. redoing read coverage parsing from samtools coverage table to sequin comment files: make_sequin_cmts.py

2. Adding read coverage to summary table. Adding virus gcode to virus summary table: virus_summary.py

3. Fixing minor error/warning when trying to create a directory that exists: assess_virus_genes1.py

4. adding sequencing tech argument--seqtech

5. Added/integrated a new taxonomy database hallmark. This database is compiled from: 1) genbank nr clustered -> extracting virus proteins with taxonomical labels for genus, family, and class -> filtering to seqs with CT3 hallmark gene hits -> reclustering at 90% AAI with cd-hit and 2) refseq virus -> filtering to seqs with CT3 hallmark gene hits.

• a) I've found this new hallmark taxdb returns better or identical taxonomical calls to the original refseq without size/memory increase
• b) Zenodo files have been update to include this database. Zenodo DB v4.1
• c) users can choose original refseq taxdb or new hallmark db with the --taxdb flag
• d) To add the hallmark taxdb, run get_ct3_dbs -o ct3_DBs --hallmark_tax T

What's Changed

• Update3 (v3.3.0 updates) by @mtisza1 in #5

Full Changelog: v3.2.1...v3.3.0

v3.2.1 Cenote-Taker 3: In the Skeloton

Changes from v3.2.0:

1. Added -wd/--working_directory flags for specifying working directory for outputs.
2. Added pyarrow to enviroment files. Prevents pandas futurewarning.
3. Fixed downcasting in fillna() commands in python/pandas.
4. Fixed paths so that hhsuite databases are download and referred to correctly.
5. Added --genbank flag which allows users to disable genbank outputs.
6. Fixed taxonomy lineage parsing in vote_taxonomy.py in certain cases.
7. Fixed hhpred_to_table.py parsing of hhsuite output files to correctly hand CDD and PDB accessions/descriptions.
8. Updated scripts so that in annotation mode -am True (unless flag --caller adaptive) to skip unnecessary initial pyhmmer steps. This reduced runtime by about 25%.

v3.2.0 Cenote-Taker 3: Swamp Lightning

This is the first official release of Cenote-Taker 3.

Everything you loved about Cenote-Taker 2, but better and faster.