antiSMASH 6.0.0
The antiSMASH team is happy to announce the stable release of antiSMASH 6.0.0.
antiSMASH 6.0.0 increases the number of detected BGC types to 71, adds a new
cluster comparison algorithm, a TIGRFam detection module, and many other
smaller changes. For details, see the [antiSMASH 6
paper](https://doi.org/10.1093/nar/gkab335).
Detailed changes:
Alexander Kloosterman (3):
common.hmmer: allow for disabling cut-tc in searches
common.pfamdb: make logging message generic
rrefinder: add RREfinder module
Kai Blin (48):
nrps_pks_domains: Fix off-by-one errors in featute/motif translation calculations
nrps/pks: Don't crash in orderfinder if there's no complete module
main: More control over output filenames
chore: bump antiSMASH version to 6.0.0alpha1
clusterblast: Properly detect magic value used during Docker lite image build
chore: Use the most current base image for the docker dev image
config: Bump version number in config file to allow for concurrent as5/6 installs
common: Relax legal identifier rules to support '2OG-FeII_Oxy' as a profile name
common/hmm_rule_parser: Detect all rule keywords in is_a_rule_keyword() check
common/hmm_rule_parser: Add CATEGORY keyword to allow classifying protoclusters by MIBiG category
hmm_detection: Ensure rule categories are valid
hmm_detection: Add prodigiosin rule to pick up Serratia-style prodigiosin clusters
html: Allow downloading region SVGs
nrps_pks_domains: Allow downloading NRPS/PKS domain SVG
html: Allow downloading Pfam domain SVGs
html: Allow downloading the record overview SVGs
tigrfam: Add new TIGRFam detection module
html: Show PFAM and TIGR domain hits in gene details
chore: update .gitignores
hmm_detection: Use new alias system to simplify PKS rules
hmm_detection: Add rule for non-alpha poly-amino acid (NAPAA) clusters
hmm_detection: Add cluster rule for pyrrolidines
hmm_detection: Rename TfuA-related to thioamitides
hmm_detection: Rename 'fused' to 'guanidinotides'
hmm_detection: Also try to identify clusters based on RREFinder profiles
hmm_detection: LAPs can also contain an E1 type enzyme
hmm_detection: TIGR03678 is the patellamide-style precursor, a cyanobactin
hmm_detection: Rename 'bacteriocin' type to 'RiPP-like'
hmm_detection: change LAP rule to avoid false positives in cyanobactin
hmm_detection: our old 'head_to_tail' type is covered by 'sactipeptide' now
hmm_detection: Add detection rule new ranthipeptide cluster type
hmm_detection: Move some LAP-related profiles from RiPP-like to LAP
html: Lipolanthines are sort of lanthipeptides, so colour them like that
hmm_detection: detect lanthipeptide class already at cluster detection stage
hmm_detection: Detect redox cofactors like PQQ and mycofactocin
hmm_detection: Change glycocins to CATEGORY RiPP
rrefinder: Update list of RiPP products
secmet: ds-DNA is also a valid molecule type
common: Give a better error message when non-JSON inputs are passed to --reuse-results
hmm_detection: TIGR03793 detects proteusin precursors, move to the appropriate rule
hmm_detection: Avoid false positive ranthipeptide calls on thiopeptides
hmm_detection: Add detection rule for epipeptides
hmm_detection: Add rule for cyclic lactone autoinducers
hmm_detection: Add rule to detect spliceotide clusters
hmm_detection: Allow filtering supported cluster types by category
rrefinder: Dynamically get list of RiPP products from rule parser
hmm_detection: Drop a dubious part of the NRPS rule for causing false positives
chore: bump version to 6.0.0
Simon Shaw (86):
html: add an option to start the overview in compact mode
clusterblast,download_databases: update clusterblast to antiSMASH-DB v3
clusterblast: catch older formats of clusterblast database
chore: pin mypy version for consistent type checking
download_databases: remove unnecessary typing ignore
chore: remove all obsolete or typing related unused-import ignores
chore: convert all comment type hints to python 3.7 style hints
common.hmmer: convert hit dict to dataclass
genefinding: fix options test with no checks
chore: style pass
chore: upgrade pylint version
common.logs: handle newer pytest changing caplog behaviour
chore: handle biopython's removal of Alphabet in 1.78 and update
chore: bump minimum python version to 3.7
clusterfinder: remove module and references to it
secmet: remove probabilities from PfamDomains, Regions and Subregions
download_databases: remove Pfam27 as a downloaded database
clusterblast: fix SVG drawing for inputs with '.' accessions
clusterblast: add test for docker runtime mount processing
config: fix incorrect executables arg placeholder
chore: update mypy to a py3.8 compatible version
chore: fix implied removal of 'no cover' pragma for coverage
common.hmmer: fix incorrect end coordinate adjustment
common.test: add a record id option for DummyRecord
common.pfamdb: add gathering cutoffs from profiles
common.hmmer: filter overlapping hits by default
common.hmmer: make HmmerResults regeneration consistent with ModuleResults
html: remove unused and redundant cog_annotations.txt
html: add Pfam visualisation
secmet: change AntismashDomain to be a generic subclassable feature
secmet: add passthrough for domain arg for AntismashDomain
secmet: order the results of get_unique_protoclusters()
secmet: add sideload variants of protoclusters and subregions
secmet: exclude sideloaded detection rules from candidates
html: pass a full region instance rather than parts
html: make 'unknown' an actual CSS class
html: handle sideloaded CDS collections differently
config: add an arg action for comma separated paths
sideloader: add module for importing external annotations
common.hmm_rule_parser: annotate outside protoclusters if in subregions
html: update antismash.js to 0.7.0
common.hmmer: remove unnecessarily specific logging
secmet: handle biopython inserting spaces in long domain names
secmet: remove the option to set CDS sec_met qualifier to None
common.serialiser: convert result JSON before truncating existing file
chore: change 'make clean' to be more generic with diamond databases
clusterblast: move diamond db checks to common.subprocessing.diamond
secmet: add a contains method to CDSCollection
html: add per-module custom JS data exporting
cluster_compare: add new cluster comparison module
html: update antismash.js to 0.8.0
html: update javascript to 0.8.1
common.hmmer: fix documentation on build_hits
sideloader: fix incomplete help for command line arg
rrefinder: fix naming duplications for features
rrefinder: fix hits duplicating in overlapping protoclusters
common.hmm_rule_parser: fix an incorrect type
common.hmm_rule_parser: fix incorrect behaviour with 'not'
tigerfam: account for docker-mounted database dirs
cluster_compare: account for docker-mounted database dirs
html: update javascript to 0.8.2
subprocessing: fix broken f-string in diamond errors
download_databases: update to clusterblast database with fungi
common.hmm_rule_parser: fix negative score test/check
common.hmm_rule_parser: make naming test more obvious when failing
common.hmm_rule_parser: add ability to create and use aliases
common.hmm_rule_parser: remove inferiors on overlap, not just contains
common.json: add support to JS datatypes for multi-CDS modules
secmet: fix sorting in multi-CDS modules
secmet: add extra tests for multi-CDS modules
secmet: restrict multi-CDS Modules to having matching strands
secmet: add a protein location fetch per parent for modules
html: update antismash.js to 0.9.0
nrps_pks_domains: detect modules involving multiple CDS features
secmet: improve reporting for non-integer codon_start qualifiers
common.serialiser: include summary of record areas in JSON
html: silence FutureWarnings for pyScss
genefinding: handle unspecified genefinding error more cleanly
secmet: recognise lower-case DNA as valid record type
common.record_processing: avoid crashes when inputs contain formatters
sideload: improve error messages for invalid/unsuitable JSON
chore: add dev wiki link to CONTRIBUTING.md
chore: fix out of date minimum python version in CONTRIBUTING.md
chore: remove aS5 specific numbering from Dockerfile
custom_typing: include missing __iter__ prototype
common.record_processing: handle bug in macOS py3.8+ pickling config