antiSMASH 6.1.0
Introduces a new visualisation for NRPS/PKS modules along with new NRPS/PKS domains.
Updates reference databases for clustercompare's MIBiG comparison, and Pfam
detection modules.
Also includes a number of fixes and other small improvements
Detailed changes since 6.0.0:
Kai Blin (6):
nrps_pks_domains: Also detect thiocysteine lyase domains as described in doi:10.1038/s41467-021-25798-8
secmet: Allow None for the Feature.overlaps_with() check
chore: Don't create dummy CDSes with the exact same location in the modules tests
secmet: ensure that we don't add two CDSes with the exact same location
secmet: Fix locus tag duplicates even if the conflicting CDSes only overlap with a gene feature of the same name
outputs/html: Honour output_basename in the HTML page title
Simon Shaw (97):
download_databases: fix database dir not propagating to prepare_data
lanthipeptides: deconflict prepeptide feature name
sactipeptides: deconflict prepeptide feature name
thiopeptides: deconflict prepeptide feature name
lassopeptides: lassopeptides: deconflict prepeptide feature name
clusterblast: fix crash on sideloaded regions with no CDS
chore: pin biopython version to avoid incompatibility
secmet: move frameshift function to secmet.locations
secmet: fix translation generation of frameshifted CDSes
common.gff_parser: keep all features found in GFF inputs
chore: handle deprecations in jinja2 >= 3.0
html: embed mask SVGs in CSS to avoid CORS on local files
common.record_processing: catch bad qualifier warnings early
pfam2go: update Pfam GO mapping
common.pfamdb: make logging messages consistent
download_databases: update Pfam latest to 34.0
clusterblast: adjust tests to handle newer diamond versions
html: shrink javascript data size
html: allow body detail divs to have scroll bars if necessary
html: add structure for visualisation-only submodules
html: use collapsers for Pfam/Tigrfam/GO details in sidepanel
html: update antismash.js to 0.10.0
html: expand pfam drawing to cover all HMMer results
html: default generic domain view to expanded mode
nrps_pks_domains: include DH2 as a modification domain
nrps_pks_domains: annotate subtypes on ModularDomain where possible
nrps_pks_domains: add carnitine-AT domain
nrps_pks_domains: add accessor for module components
nrps_pks_domains: merge additional modules in split-CDS modules when relevant
nrps_pks_domains: include more domains in modules when relevant
nrps_pks_domains: don't register modules containing only a single domain
nrps_pks_domains: add SH domains in module/double carrier protein handling
nrps_pks_domains: add a public method to get CSS and abbreviations for domains
nrps_pks_domains: fix ModularDomain being modified post-creation by nrps_pks
nrps_pks_domains: include TIGR01720 as a special domain in modules
cluster_compare: use a minimal and updatable database for integration tests
nrps_pks: add candidate kind to layer
nrps_pks: make result schema version public
nrps_pks: use starter/final module status instead of specific domains
html: add modular domain 'bubble' visualiser
secmet: add members for area product category/categories
hmm_detection: pass product category to created protoclusters
chore: change 'will_handle()' to also take categories
hmm_detection: fix linaridin category and add description
html: allow fallback to rule category for CSS if no CSS for product
rrefinder: use product categories to test if a cluster is a RiPP
sideloader: add string functions for result types
sideloader: pass full record through to result generation
sideloader: require all sideloaded areas to have at least one CDS
config: add an action for splitting comma separated lists in args
sideloader: add options for creating arbitrary subregions around CDSes by name
main: auto-import analysis modules
genefinding: move from 'detection' namespace to 'support'
main: automatically detect, import, and use detection modules
main: split --list-plugins into sections based on detection stage
main: remove unreachable returns and raises
chore: handle pylint 'consider-using-with' message where possible
chore: consistently use 'from ... import ...' style
chore: remove unused imports and context handlers
clusterblast: clean up test file read logic
hmm_detection: remove code for python < 3.5 from tests
hmm_detection: add missing docstrings for categories
common.hmm_rule_parser: fix accidental concatenation in test strings
cluster_compare: fix ineffective order scaling test
html: fix variable name shadowing import name
secmet: remove shadowed import in region
secmet: add missing docstring to AntismashDomain subtype handling
chore: style pass for misc pylint 2.10 messages
chore: update pinned pylint version to 2.10.2
html,common.layers: fix circular import
full_hmmer: fix missing typing in data rebuild script
chore: satisfy flake8 whitespace
nrps_pks_domains: remove code duplication in tests
cassis: break circular dependency on config constants
chore: update mypy to 0.910
chore: bump version to 6.1.0
chore: add a github action for comparing pull requests
chore: use more permissive mode for linting action
domain_identification: prevent cross-CDS modules forming when interrupted
html: update antismash.js to 0.10.1
html: fix crash when regions contain no protoclusters
html: add test for records without protoclusters
nrps_pks: fix non-colinear CDS ordering when cross-CDS modules are involved
nrps_pks: fix polymer formation duplicating monomers from cross-CDS modules
nrps_pks: don't include chained CDS features in domain-docking count limit
html: truncate cross-CDS modules in bubble view when not fully in candidate
html: update antismash.js to 0.11.0
html: fix hybrid region CSS
sactipeptides: remove unused genbank in tests
lanthipeptides: avoid duplication of found CDS features
sactipeptides: avoid duplication of found CDS features
thiopeptides: avoid duplication of found CDS features
lassopeptides: avoid duplication of found CDS features
cluster_compare: change data sources in MIBiG DB building
cluster_compare: fix MIBiG DB generation for 'Other' subclass
cluster_compare: don't include post-detection gene functions in databases
download_databases: update clustercompare database version