This is release 5.2.0 of antiSMASH.
Highlights are:
* added detection for lanthidine clusters
* improved detection of thioamide-NRP clusters
* updates the default PFAM database to 32.0, with matching GO term update
* updates the clusterblast database to the antiSMASH-DB version 3
* PKS candidate clusters with products determined by non-colinear gene ordering now record and show the order used
* a new command line option `--html-start-compact`, which defaults the HTML overview to the compact view
**NOTE:** As the antiSMASH-DB links have changed slightly to be more future proof, the clusterblast database format has also changed slightly to take advantage of that. It is necessary to update the clusterblast database at the same time as updating to 5.2 from previous versions.
This can be done by running the command `download-databases` when antiSMASH is installed in your environment (or `antismash/download-databases.py` in the source directory). There is also a direct download of the database tarball available [here](https://dl.secondarymetabolites.org/releases/clusterblast/clusterblast_20201012.tar.xz).
Detailed changes:
Kai Blin (11):
nrps_pks_domains: Also detect SMART PKS_PP domain as ACP
main: Bump the antiSMASH version logging line to INFO level
chore: Bump version to 5.2.0
common: Fix the java version detection when _JAVA_OPTIONS are set
config: fix alternative fasttree executable spelling
hmm_detection: Improve thioamide-NRP rules to pick up more clusters
detection: Add detection rule for lanthidines
chore: Pin Biopython to 1.76, as 1.77 refuses to work with still support Python 3.5
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
Simon Shaw (40):
secmet: fix region genbank outputs not adjusting locations in qualifiers
nrps_pks_domains: allow AT and CP without KS to be complete module
nrps_pks_domains: only allow condensationless modules to be complete if first in a CDS
common.record_processing: include record id in error message
html: remove duplicate mod-kr CSS rule
secmet: handle genbank conversions introducing spaces into aSDomains
*peptides: import joblib directly for future scikit-learn versions
secmet: replace minimock usage with unittest
lassopeptides: replace minimock usage with unittest
active_site_finder: replace minimock usage with unittest
t2pks: replace minimock usage with unittest
nrps_pks: replace minimock usage with unittest
clusterblast: replace minimock usage with unittest
cassis: replace minimock usage with unittest
antismash.test: remove unnecessary mocking
pfam2go: replace minimock usage with unittest
nrps_pks: replace minimock usage with unittest
cluster_hmmer: replace minimock usage with unittest
full_hmmer: replace minimock usage with unittest
lanthipeptides: replace minimock usage with unittest
thiopeptides: replace minimock usage with unittest
antismash.test: replace minimock usage with unittest
chore: remove minimock as a test dependency
secmet: remove list inheritance from NRPSPKSQualifier
secmet: improve error message for invalid translation table qualifiers
common: only check relevant parts in RODEO's sklearn version check
hmm_detection: find more transAT-PKS clusters
pfam2go: update GO mapping
download_databases: update to 32.0 for latest Pfam database
common.record_processing: conditionally allow long record identifiers
clusterfinder: fix subregions being added twice
thiopeptides: fix results regeneration for extra ORFs
t2pks: only use CDSs completely within the protocluster