You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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.
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
This discussion was created from the release antiSMASH 6.0.0.
reacted with thumbs up emoji reacted with thumbs down emoji reacted with laugh emoji reacted with hooray emoji reacted with confused emoji reacted with heart emoji reacted with rocket emoji reacted with eyes emoji
-
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.
Detailed changes:
This discussion was created from the release antiSMASH 6.0.0.
Beta Was this translation helpful? Give feedback.
All reactions