v2.0.0-beta.3

What's Changed

• config hash only relevant values by @nlouwen in #234
• Hotfix/cleanup by @nlouwen in #235
• split tests from badges workflow by @adraismawur in #236
• Fix the pytest repo badge and add a badge for the docker deployment workflow by @adraismawur in #238
• Add temporary tables for GBK file hashes and GBK ids by @adraismawur in #239

Full Changelog: v2.0.0-beta.2...v2.0.0-beta.3

v2.0.0-beta.2

What's Changed

• remove release/ from new version by @adraismawur in #231
• update the mibig-version help text by @adraismawur in #232

Full Changelog: v2.0.0-beta.1...v2.0.0-beta.2

v2.0.0-beta.1

This version is still in pre-release and is undergoing testing.

The repository is also subject to change.

Major

BiG-SCAPE 2 Workflows.

The BiG-SCAPE logic has been separated into three workflows:

• BiG-SCAPE Cluster: Most common use case, performs distance calculations and clustering of BGCs.
• BiG-SCAPE Query: Uses the logic in BiG-SCAPE Cluster to return all BGCs that show similarity to a user defined Query BGC.
• BiG-SCAPE Benchmark: Allows benchmarking of the clustering/GCF calling of a given run/set of runs against a user provided curated set of GCF assignments.

Record and edge types

• Allows selection of any antiSMASH record type (region, candidate cluster, protocluster, protocore) as the working record to be used throughout the run.
• Each record will be showcased as a node in the sequence similarity network, and, when relevant, topo-links/edges (dashed lines) are shown between records that originate from the same region.
• Protoclusters/Protocores within interleaved and chemical hybrid candidate clusters are merged into one record.

BiG-SCAPE Classes & Weights

• Added classification based on antiSMASH Class and Category, in addition to BiG-SCAPE 1’s legacy classification. BiG-SCAPE 2’s default is to classify based on antiSMASH Category.
• BiG-SCAPE 1’s legacy classification into 8 groups remains compatible with antiSMASH versions up to v7.
• BiG-SCAPE 1’s legacy weight distribution of each distance component can be paired with the legacy classification mode, as well as new antiSMASH-based classification (for antiSMASH versions v6 and up).

Input & References

• A user-defined reference set of (antiSMASH processed) .gbks can be provided.
• Using the --mibig-version [version_number] flag will (if necessary) download and use antiSMASH processed MIBiG versions 3.1 and up.
• MIBiG .gbks are now available already processed by a custom antiSMASH version that ensures that MIBiG .gbks that would not trigger an antiSMASH rule are still processed, and BiG-SCAPE will download these directly from the https://dl.secondarymetabolites.org/mibig/ webpage.
• Any custom antiSMASH processed set of MIBiG .gbk files can also be provided.
• .gbks which were not processed by antiSMASH, but that do contain CDS and Sequence features can be provided by using the --force-gbk flag. Note: beta state, use with caution.

Output & Database usage

• Replaced all intermediary files with an SQLite database.
• An already populated SQLite database can be provided such that all relevant information, i.e. records and edges that are present in the input folder, can be reused.
• Canceled runs retain data on disc to continue from on re-run.
• Added an option to run entirely in-memory to reduce runtime.
• Added a full .network file, which contains all calculated distances without any cutoffs applied. Distances = 1 are not included.
• Removed independently generated arrower.py SVGs of each individual .gbk.
• Removed Clans, a second layer of clustering to attempt to group families into clans.

Full Changelog: v1.1.9...v2.0.0-beta.1

v1.1.9

What's Changed

• fix setup by @paulzierep in #127

Full Changelog: v1.1.8...v1.1.9

v1.1.8

What's Changed

• Little fix for recipe by @SantaMcCloud in #118
• Revert "Little fix for recipe" by @adraismawur in #120
• fix bgc_data import issue by @paulzierep in #122
• bump version numbers by @adraismawur in #123

New Contributors

• @SantaMcCloud made their first contribution in #118
• @paulzierep made their first contribution in #122

Full Changelog: v1.1.7...v1.1.8

BiG-SCAPE 1.1.7

What's Changed

• Fix module issues by @adraismawur in #93

Full Changelog: v1.1.6...v1.1.6b

BiG-SCAPE 1.1.6

What's Changed

• Feature/docker by @CatarinaCarolina in #28
• copy colors file to output directory instead of replacing working dir copy by @adraismawur in #54
• Fix setup.py packaging, making bigscape installable by @pettyalex in #76

New Contributors

• @pettyalex made their first contribution in #76

Full Changelog: v1.1.5...v1.1.6

BiG-SCAPE 1.1.5

• Adds MIBiG 3.1 BGCs as reference (now the default for --mibig)
• Added rules for 'prodigiosin' (PKS Other), 'mycosporine-like' (Other) and 'crocagin' (RiPP)
• Officially dropped Python 2 support
• Code Cleanup

v1.1.4

What's Changed

• Setup data_files by @loraine-gueguen in #4
• Remove indent by @loraine-gueguen in #6
• Fix packaging issue by @loraine-gueguen in #8

New Contributors

• @loraine-gueguen made their first contribution in #4

Full Changelog: v1.1.3...v1.1.4

v1.1.3

fixed a small by-one bug when parsing hmmer data