v2.0.3

What's Changed

• chore/citations by @nlouwen in #333
• Bugfix/review-collection by @nlouwen in #335
• Hotfix/mibig-input by @nlouwen in #336

v2.0.2

What's Changed

• fix pyhmmer 12 breaking changes by @adraismawur in #331
  • Thanks to @althonos for the advice in fixing this one

Full Changelog: v2.0.1...v2.0.2

v2.0.1

What's Changed

• Removed broken badges gh action by @adraismawur in #318
• Fix docker action by @adraismawur in #319
• Merge master to dev by @adraismawur in #326
• replace pkg_resources with importlib_resources by @adraismawur in #327
• Update cluster_cli.py by @mmzdouc in #324

New Contributors

• @mmzdouc made their first contribution in #324

Full Changelog: v2.0.0...v2.0.1

v2.0.0

What's Changed

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.
• BiG-SCAPE Dereplicate: Performs clustering and de-replication of BGCs to reduce input dataset size using Sourmash

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.

2.0.0rc8 bioconda

Bioconda obeys the python packaging version specifier constraints, which limits the specific format that version numbers can be in.

I have very, very strong opinions about this. But I am not one to fight against the waves.

Instead this is one of the specific tags just to accommodate this limitation. It is otherwise identical to v2.0.0-beta.8

v2.0.0-beta.8 release for zenodo

What's Changed

• hotfix/html genome count by @nlouwen in #304
• Removed some unused badges from the readme

Full Changelog: 2.0.0-beta.7...v2.0.0-beta.8

v2.0.0-beta.8

What's Changed

• hotfix/html genome count by @nlouwen in #304
• Removed some unused badges from the readme

Full Changelog: 2.0.0-beta.7...v2.0.0-beta.8

2.0.0-beta.7

What's Changed

• Hotfix/performant results gen by @adraismawur in #290
• remove erroneous env_from trimming from simple hmmsearch implementation by @adraismawur in #289
• add option to switch subprocess spawn method by @adraismawur in #274
• Rename all instances of hmmscan to hmmsearch by @adraismawur in #291
• remove unused config initialization by @nlouwen in #298
• Topic/derep by @CatarinaCarolina @nlouwen in #299

Full Changelog: v2.0.0-beta.6...2.0.0-beta.7

v2.0.0-beta.6

What's Changed

• clarify gbk parsing errors. again. by @adraismawur in #264
• add gutsmash version parsing by @nlouwen in #265
• Hotfix/caner insert batching by @adraismawur in #267
• only search for mibig to download if not already present by @CatarinaCarolina in #275
• switch columns in node selection download and add edge selection download by @CatarinaCarolina in #276
• add fair badge by @adraismawur in #280
• add output temp tables by @adraismawur in #281
• Feature/load gbk faster by @adraismawur in #273

Full Changelog: v2.0.0-beta.5...v2.0.0-beta.6

v2.0.0-beta.5

What's Changed

• hotfix/mibig-4-compatibility by @nlouwen in #254
• Hotfix/cand cluster category by @nlouwen in #253
• hotfix/index-bgc-count by @nlouwen in #257
• Hotfix/reformat tsv by @nlouwen in #256

Full Changelog: v2.0.0-beta.4...v2.0.0-beta.5