antiSMASH 5.1.0
Introduces NRPS/PKS modules, a new TfuA-related RiPP cluster type, and a new
fungal PKS domain. The knownclusterblast database has been updated to the
latest MIBiG release (2.0).
Detailed changes since 5.0.0:
Kai Blin (6):
chore: Add config for no-response probot plugin
hmm_detection: Adjust Chal_sti_synth_* profile cutoffs to cutoff values given in files
detection: Add TfuA-related clusters
nrps_pks_domains: Identify fungal non-reducing PKS product template (PT) domains
secmet: Python 3.7 no longer escapes :
chore: use os.path.realpath to fix path tests on OSX
Simon Shaw (96):
clusterblast: fix SVG colouring missing when hits have same accession
clusterblast: don't exclude self-hits in SVGs for subclusterblast
nrps_pks_domains: add a trusted cutoff for Enedyne_KS to match other KSs
common.record_processing: include NRPS_PKS qualifier in stripping step
common.record_processing: use secmet stripping function after conversion
html: update antismash.js to 0.4.2
common.hmmer: remove broken check
secmet: restrict protocluster products to same style as ruleset
common.record_processing: differentiate between no records found and records too small
hmm_detection: improve reuse handling of strictness option
html: hide detection rule section when no rule-based clusters present
secmet: always pass through a Seq to Record's inner SeqRecord
html: make output less horrific for slow loading or missing CSS
common.record_processing: fix loss of record annotations with --start or --end
main: improve genbank meta-comment annotation
common.record_processing,gff_parser: read GFF input only once for features
common.record_processing: log error details when present for bad GFFs
html: use correct header border colour based on variant
config: allow testing error messages from arg parsing
config: add an arg action to ensure paths are readable
config,*: use path actions where appropriate
clusterblast: fix SVGs generating with extra end anchor links
nrps_pks_domains: don't create an empty HTML tab, similar to monomers/compounds
html: update antismash.js to 0.4.3
__main__: change git version to use source dir, not working dir
html: fix header/footer images with overridden sizes
html: update antismash.js to 0.4.4
secmet: alter genefunction tool priority
html: change resistance gene visualisation to a marker under the gene
html: add a symbol based legend macro
html: change resistance and TTA legends to use their symbols
secmet: add a test for gene function qualifier conversion
secmet: track child core location for candidate clusters
secmet: allow sorting comparisons of features and locations
secmet: prevent orphaning and inconsistent grouping of protoclusters
setup.py: fix pytest version to solve coverage issues
antismash.test: shift global --check-prereqs unit test to integration
chore: silence deprecation warnings within pyScss during testing
chore: re-silence Cython warnings silenced by numpy and unsilenced by pytest
hmm_detection: log strictness level
html: add hmm_detection strictness to overview page
secmet: handle biopython/genbank conversions losing spaces in qualifiers
secmet: handle bad codon errors in CDS translation
secmet: fix outdated docstring
secmet: include record ID in text for bad locations
html: use a serif font for CDS names
html: fix single pixel header tab underline in edge
config: don't report 'does not exist' if the target is a directory
secmet: fix candidate creation issue with multiple fully-contained non-hybrids
chore: clean pickled classifiers and add them to ignore
chore: silence mypy errors in externally provided code
common.external: add a simplified pickle function for rodeo
lanthipeptides: rebuild classifier in prepare_data
lassopeptides: rebuild classifier in prepare_data
thiopeptides: rebuild classifier in prepare_data
sactipeptides: rebuild classifier in prepare_data
chore: unpin scikit-learn version
lassopeptides: change to standard copyright/license header
common.test: bring in more helper classes from secmet
common.hmmscan_refinement: allow comparisons and hashing of HMMResult
secmet: add missing SubRegion __slots__
secmet: fix cdscollection typing issue
secmet: make from_biopython conversion interface consistent
secmet: make Record's adding of biopython features consistent
secmet: simplify postponed feature logic
secmet: add support for explicit int conversion in parse_format
secmet: support subtypes in NRPS/PKS domains
secmet: enforce Domains having locus tag and protein location
html,nrps_pks_domains: move styling and abbreviating domains from javascript to CSS/python
common.json: add abbreviations for Aminotran domains
common.json: don't colour ACPS domains
html: make heights of single feature domain SVGs and all feature SVGs match
nrps_pks: remove unnecessary END from SMILES set
nrps_pks: fix pks smiles replacement being overeager
nrps_pks_domains: remove duplicate add_to_record
secmet: add Module feature
nrps_pks_domains,nrps_pks: add module identification and visualisation
nrps_pks_domains: add PP-binding as a fallback for *CP profiles
nrps_pks_domains: show a question mark on HTML modules if unknown substrate
nrps_pks: use lower case for smiles to reduce duplication
nrps_pks: assign smiles even if only one monomer is present
nrps_pks: update SMILES values and format
html: reduce size of serif CDS names in NRPS domains tab
nrps_pks: display Stachelhaus codes with serif font
nrps_pks_domains: fix error message using incorrect count
nrps_pks_domains: move DummyHMMResult to common test helpers
nrps_pks_domains: consolidate matching of PKS_KS domains to their subtypes
nrps_pks: fix error with X monomer substitutions
secmet: fix inconsistent sorting in interleaved candidate construction
nrps_pks: add SMILES parser/reconstructor
nrps_pks: add methylation logic
nrps_pks: refactor SMILES generation
common.hmmer: catch missing hmmpress before attempts to use it
clusterblast: catch missing diamond before attempting to use it
antismash.test: ensure check-prereqs fails gracefully
chore: bump version to 5.1.0
Zach Charlop-Powers(2):
Remove Unused Args from Function Docs
Use os.makedirs instead of os.mkdir