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Recent Releases of autometa

autometa - Release 2.2.3

  • Fix "TypeError: boolean value of NA is ambiguous" Issue #360 in #361 by @chasemc and @Sidduppal

Full Changelog: https://github.com/KwanLab/Autometa/compare/2.2.2...2.2.3

- Python
Published by Sidduppal over 1 year ago

autometa - Release 2.2.2

What's Changed

  • :arrow_up: bump readthedocs-sphinx-search; 0.1.1 to 0.3.2 by @chasemc in https://github.com/KwanLab/Autometa/pull/354
  • 🐛 Fixes Biopython deprecation warning by @Sidduppal in #350
  • Fix "ncbi rsync error when downloading markers" #347 in #352 by @Sidduppal
  • :arrow_up: Pin BioPython to >=1.82
  • :arrow_up: Pin Pandas to >=1.5
  • Release 2.2.2 by @Sidduppal in https://github.com/KwanLab/Autometa/pull/359

Full Changelog: https://github.com/KwanLab/Autometa/compare/2.2.1...2.2.2

- Python
Published by Sidduppal over 1 year ago

autometa - Release 2.2.1

What's Changed

  • 🧑‍🔧 📝 Fix docs by @Sidduppal in https://github.com/KwanLab/Autometa/pull/323
  • Step by step walkthrough by @kaw97 in https://github.com/KwanLab/Autometa/pull/314
  • 🎨 🍏 Issue 330 redo by @shaneroesemann in https://github.com/KwanLab/Autometa/pull/338
  • :fire::whale::green_heart: Fix docker-builds by removing pinned dependencies by @WiscEvan in https://github.com/KwanLab/Autometa/pull/340
  • singularity image urls by @kaw97 in https://github.com/KwanLab/Autometa/pull/316
  • helpful error message added by @RajnishProgrammer in https://github.com/KwanLab/Autometa/pull/307
  • 💚:bug::snake: Fix bug for 0 passing predictions by @WiscEvan in https://github.com/KwanLab/Autometa/pull/341
  • :bug: Fix GTDB database setup by @Sidduppal in https://github.com/KwanLab/Autometa/pull/329
  • :bug::shell: Fix GTDB taxon-binning workflow by @shaneroesemann in https://github.com/KwanLab/Autometa/pull/339
  • 📝 Update documentation by @WiscEvan in https://github.com/KwanLab/Autometa/pull/342
  • :snake::art::fire::bug: Fix UnboundLocalError bug by @WiscEvan in https://github.com/KwanLab/Autometa/pull/325
  • :bug::art::snake: Refactor 'unclassified' handling by @kaw97 and @WiscEvan in https://github.com/KwanLab/Autometa/pull/343
  • Release 2.2.1 by @WiscEvan in https://github.com/KwanLab/Autometa/pull/344

New Contributors

  • @RajnishProgrammer made their first contribution in https://github.com/KwanLab/Autometa/pull/307

Full Changelog: https://github.com/KwanLab/Autometa/compare/2.2.0...2.2.1

- Python
Published by WiscEvan over 2 years ago

autometa - Release 2.2.0

Release 2.2.0

Breaking changes 💣 💔🙈

Autometa's autometa-taxonomy and autometa-binning-summary entrypoints (instead of taking --ncbi as an input parameter) now take --dbdir and --dbtype to allow the user to use either the NCBI or GTDB database.

| Command | 💔 Previous 💔 | 💚 New 💚 | |:--------------------------:|:------------:|--------------------------------------------------------------------------| | autometa-taxonomy | --ncbi | --dbdir <ncbi-database-dirpath>, --dbtype ncbi (choices: ncbi, gtdb) | | autometa-binning-summary | --ncbi | --dbdir <ncbi-database-dirpath>, --dbtype ncbi (choices: ncbi, gtdb) |

NOTE: For implementation details for integrating other taxonomy databases see https://github.com/KwanLab/Autometa/pull/284

🐚 Additional autometa workflows

  • Addition of workflow where only required inputs are reads and assembly
  • autometa.sh and autometa-large-data-mode.sh now require taxa_routine as an input parameter (choices are "ncbi" or "ncbi_gtdb". Autometa workflow now contains an optional sub-workflow where binning is guided by GTDB taxonomy after retrieving bacteria and archaea classified using the NCBI database.

TaxonomyDatabase

:snake: GTDB taxonomy integration to use within Autometa's taxon-binning and genome-binning workflows.

For more information on GTDB database setup see the Autometa GTDB database documentation

```bash (autometa) evan@userserver:~/Autometa$ autometa-setup-gtdb -h usage: autometa-setup-gtdb [-h] --reps-faa REPS_FAA --dbdir DBDIR [--cpus CPUS]

optional arguments: -h, --help show this help message and exit --reps-faa REPS_FAA Path to directory containing GTDB ref genome animo acid data sequences. Can be tarballed. --dbdir DBDIR Path to output GTDB database directory --cpus CPUS Number of cpus to use for diamond-formatting GTDB database ```

TL;DR

Abstraction of taxonomy databases using TaxonomyDatabase abstract base class with required abstractmethods.

This is currently implemented for both the NCBI and GTDB taxonomy database. Future taxonomy database integrations should follow the format from the TaxonomyDatabase class.

CAMI formatter

Binning validation/benchmarking utilities added/updated such as formatting autometa binning results into biobox format

Misc

  • 💚 Fix pytest requirements in GH actions
  • :bug:⬇️ pin scipy and joblib to avoid hdbscan import error
  • :snake:🤫 Fix deprecated pandas method invocation in bedtools.py

What's Changed

  • :memo: Added contribution documentation by @jason-c-kwan in https://github.com/KwanLab/Autometa/pull/277
  • :art::snake: Add CAMI formatter entrypoint autometa-cami-format by @WiscEvan in https://github.com/KwanLab/Autometa/pull/276
  • :art::snake: Update deprecated pandas method invocation by @WiscEvan in https://github.com/KwanLab/Autometa/pull/279
  • ⬇️ 💚 force scipy==1.8 by @kaw97 in https://github.com/KwanLab/Autometa/pull/286
  • :shell: New bash files for Autometa workflow by @samche42 in https://github.com/KwanLab/Autometa/pull/281
  • ⬆️ 🎨 Allow the use of gtdb taxonomy in Autometa by @Sidduppal in https://github.com/KwanLab/Autometa/pull/284
  • Add --average-method parameter to autometa-benchmark by @WiscEvan in https://github.com/KwanLab/Autometa/pull/290
  • GTDB integration by @Sidduppal and @WiscEvan in https://github.com/KwanLab/Autometa/pull/284

New Contributors

  • @jason-c-kwan made their first contribution in https://github.com/KwanLab/Autometa/pull/277
  • @kaw97 made their first contribution in https://github.com/KwanLab/Autometa/pull/286

Full Changelog: https://github.com/KwanLab/Autometa/compare/2.1.0...2.2.0

- Python
Published by WiscEvan about 3 years ago

autometa - 2.1.0

[2.1.0] - 2022-05-12

Added

  • :snake:autometa entrypoint to retrieve info on --citation, --version and no argument lists other autometa commands
  • :green_apple: The autometa version is written after completion of each autometa-related nextflow process
  • :shell: The autometa version is emitted at the beginning of the autometa bash workflow.
  • :snake: NCBI.py will now search delnodes.dmp for any taxids retrieved from blast output and convert to root (taxid=1)

Fixed

  • :shell::bug: Renamed incorrect variables $coverage to $coverages and $clustering_method to $cluster_method in workflows/autometa.sh
  • :snake::bug: Fix use of kwargs in kmers embed(..., *kwargs) function
  • :snake::bug: Fix passing n_jobs to kmers embed(..., n_jobs=1) function
  • 🍏 :whale:Add params.autometa_image_tag to mock_data_reporter process
  • 🍏 🐳 Add params.autometa_image_tag to get_genomes_for_mock process

Dependencies

  • :arrowup::greenheart: Pinned black version to 22.3.0
  • ⬆️:green_apple: upgrade diamond to version 2.0.14

Removed

  • :fire::green_heart: Removed tests/requirements.txt and consolidated to tests/environment.yml

What's Changed (from the git logs)

  • :art::snake: Add taxid conversion from 'unclassified' to 1 for taxon-profiling benchmarking by @WiscEvan in https://github.com/KwanLab/Autometa/pull/260
  • :memo: Update installation directions for bash workflow by @WiscEvan in https://github.com/KwanLab/Autometa/pull/262
  • :snake::bug: Fix parsing taxids to delnodes set by @WiscEvan in https://github.com/KwanLab/Autometa/pull/265
  • :arrowup: :greenapple: Upgrade Diamond 2.0.9 -> 2.0.14 by @chasemc in https://github.com/KwanLab/Autometa/pull/264
  • :art::bug::snake: Add n_jobs to embed(...) func. Replace **method_args w/ **method_kwargs by @WiscEvan in https://github.com/KwanLab/Autometa/pull/267
  • Versioning by @WiscEvan in https://github.com/KwanLab/Autometa/pull/269
  • :art::green_apple: Add autometa --version to autometa nextflow files by @WiscEvan in https://github.com/KwanLab/Autometa/pull/271
  • :bug::shell: Fix variable name for autometa-binning-summary by @WiscEvan in https://github.com/KwanLab/Autometa/pull/272
  • Release 2.1.0 by @WiscEvan in https://github.com/KwanLab/Autometa/pull/273

Full Changelog: https://github.com/KwanLab/Autometa/compare/2.0.3...2.1.0

- Python
Published by WiscEvan almost 4 years ago

autometa - 2.0.3

What's Changed

  • :memo: Add CITATION file by @shaneroesemann in https://github.com/KwanLab/Autometa/pull/242
  • :bug::art::green_apple: Allow utf-8-sig sample sheets #250
  • :bug::memo::green_apple: Replace incorrect runtime defaults specified in nf-core launch command #252
  • :art::green_apple: Continue nextflow workflow (without termination) if bins are not recovered from a particular dataset #253
  • :art::bug: autometa-benchmark entrypoint, when checking taxid classifications, now converts any taxids of 0 to 1 #254
  • :bug: NCBI connection is checked prior to NCBI database files download rather than pinging google DNS #258
  • :bug: Fix autometa-length-filter bug where specifying a directory when writing to --output-fasta was required (now optional) #256
  • 💚 ⬆️:whale::green_apple: Bump version to 2.0.3 in VERSION and manifest.version in nextflow.config s.t. autometa docker images used in nextflow workflow correspond to most recent release

New Contributors

  • @shaneroesemann made their first contribution in https://github.com/KwanLab/Autometa/pull/242

Full Changelog: https://github.com/KwanLab/Autometa/compare/2.0.2...2.0.3

- Python
Published by WiscEvan almost 4 years ago

autometa - 2.0.2

What's Changed

  • :bug: Fix the NoneType error during initating the LCA object (#246) by @chtsai0105 in https://github.com/KwanLab/Autometa/pull/247

New Contributors

  • @chtsai0105 made their first contribution in https://github.com/KwanLab/Autometa/pull/247

Full Changelog: https://github.com/KwanLab/Autometa/compare/2.0.1...2.0.2

- Python
Published by WiscEvan almost 4 years ago

autometa - 2.0.1

What's Changed

  • Environment and directory structure updates by @WiscEvan in https://github.com/KwanLab/Autometa/pull/8
  • resolved #10 Contributors added and copyright year updated to 2020. by @WiscEvan in https://github.com/KwanLab/Autometa/pull/15
  • Resolving issues #16, #17, #18, #21 and update to Autometa API and Logger by @WiscEvan in https://github.com/KwanLab/Autometa/pull/25
  • Resolved #19 added docstring, fixed nproc and removed depth function by @Sidduppal in https://github.com/KwanLab/Autometa/pull/29
  • Documentation by @Sidduppal in https://github.com/KwanLab/Autometa/pull/34
  • Issue #5 Working conda recipe by @WiscEvan in https://github.com/KwanLab/Autometa/pull/38
  • 🐛found in coverage by @WiscEvan in https://github.com/KwanLab/Autometa/pull/49
  • fixes #2 by @WiscEvan in https://github.com/KwanLab/Autometa/pull/47
  • Contributing Guidelines by @WiscEvan in https://github.com/KwanLab/Autometa/pull/50
  • Add Markers class documentation. by @WiscEvan in https://github.com/KwanLab/Autometa/pull/62
  • Add main.py documentation (fixes #60) by @WiscEvan in https://github.com/KwanLab/Autometa/pull/63
  • Add functionality to bin without taxonomy. Update docstrings by @WiscEvan in https://github.com/KwanLab/Autometa/pull/65
  • Documentation by @Sidduppal in https://github.com/KwanLab/Autometa/pull/45
  • Remove merge conflict resolution lines (Fixes #68) by @WiscEvan in https://github.com/KwanLab/Autometa/pull/69
  • :art::bug: Add mock import of modules and link to contribution guidelines (fixes #22) by @Sidduppal in https://github.com/KwanLab/Autometa/pull/70
  • Resolves #55 Environ by @Sidduppal in https://github.com/KwanLab/Autometa/pull/76
  • fixes-#54 Metagenome by @WiscEvan in https://github.com/KwanLab/Autometa/pull/66
  • Update MAG class to MetaBin by @WiscEvan in https://github.com/KwanLab/Autometa/pull/67
  • hmmer by @Sidduppal in https://github.com/KwanLab/Autometa/pull/72
  • LCA by @WiscEvan in https://github.com/KwanLab/Autometa/pull/78
  • Fix writing by @WiscEvan in https://github.com/KwanLab/Autometa/pull/82
  • Update majority_vote by @WiscEvan in https://github.com/KwanLab/Autometa/pull/81
  • pre-commit hooks by @WiscEvan in https://github.com/KwanLab/Autometa/pull/92
  • verbose bug by @WiscEvan in https://github.com/KwanLab/Autometa/pull/90
  • Recursive DBSCAN by @WiscEvan in https://github.com/KwanLab/Autometa/pull/84
  • databases and utilities by @WiscEvan in https://github.com/KwanLab/Autometa/pull/77
  • Rank-specific binning by @WiscEvan in https://github.com/KwanLab/Autometa/pull/96
  • diamond.py by @Sidduppal in https://github.com/KwanLab/Autometa/pull/87
  • Add support request issue template. by @WiscEvan in https://github.com/KwanLab/Autometa/pull/97
  • ncbi.py by @Sidduppal in https://github.com/KwanLab/Autometa/pull/83
  • Samtools by @Sidduppal in https://github.com/KwanLab/Autometa/pull/103
  • Binning stats/taxonomy summary by @WiscEvan in https://github.com/KwanLab/Autometa/pull/99
  • decision tree classifier by @WiscEvan in https://github.com/KwanLab/Autometa/pull/100
  • Fix config and setup of user project by @WiscEvan in https://github.com/KwanLab/Autometa/pull/104
  • Update project docstrings by @WiscEvan in https://github.com/KwanLab/Autometa/pull/108
  • CI/CD by @WiscEvan in https://github.com/KwanLab/Autometa/pull/101
  • :bug: Change > to >= when calculating N50 by @chasemc in https://github.com/KwanLab/Autometa/pull/119
  • Fix Dockerfile by @WiscEvan in https://github.com/KwanLab/Autometa/pull/123
  • Add support for gzipped assemblies by @WiscEvan in https://github.com/KwanLab/Autometa/pull/129
  • Update bug report template by @WiscEvan in https://github.com/KwanLab/Autometa/pull/130
  • Remove --multiprocess from autometa-kmers entrypoint by @WiscEvan in https://github.com/KwanLab/Autometa/pull/127
  • Add GC content std.dev. limit and coverage std. dev. limit Binning metrics by @WiscEvan in https://github.com/KwanLab/Autometa/pull/120
  • Nextflow implementation template by @WiscEvan in https://github.com/KwanLab/Autometa/pull/118
  • Update documentation by @Sidduppal in https://github.com/KwanLab/Autometa/pull/121
  • Add feature to download google drive datasets by @ajlail98 in https://github.com/KwanLab/Autometa/pull/138
  • Add densmap embed method and fix binning-summary cluster column bug by @WiscEvan in https://github.com/KwanLab/Autometa/pull/176
  • Classification and Clustering Benchmarking by @WiscEvan in https://github.com/KwanLab/Autometa/pull/141
  • Nfcore and structuring modules for collaboration by @chasemc in https://github.com/KwanLab/Autometa/pull/157
  • Delete .gitattribute - there is a .gitattributes by @chasemc in https://github.com/KwanLab/Autometa/pull/190
  • :fire::green_apple: Remove duplicate standard slurm profiles by @WiscEvan in https://github.com/KwanLab/Autometa/pull/195
  • Fix import error in databases.py by @WiscEvan in https://github.com/KwanLab/Autometa/pull/194
  • Fix/Create mock data subworkflow by @chasemc in https://github.com/KwanLab/Autometa/pull/206
  • 🐳:bug: Docker fix :whale: by @WiscEvan in https://github.com/KwanLab/Autometa/pull/213
  • :memo: Update Documentation by @WiscEvan in https://github.com/KwanLab/Autometa/pull/212
  • :art: Add typehints and update kmers docstring by @WiscEvan in https://github.com/KwanLab/Autometa/pull/208
  • :art::snake: Add specific parsers for domtblout and tblout for hmmscan output formats by @WiscEvan in https://github.com/KwanLab/Autometa/pull/201
  • :snake::art::bug: Update metagenome.length_filter(...) by @WiscEvan in https://github.com/KwanLab/Autometa/pull/210
  • Fix bedtools genomecov deprecation (coverage calculation) by @WiscEvan in https://github.com/KwanLab/Autometa/pull/209
  • :art:🐚 Add bash-implementations of Autometa workflows by @WiscEvan in https://github.com/KwanLab/Autometa/pull/202
  • Nextflow documentation by @chasemc in https://github.com/KwanLab/Autometa/pull/184
  • :fire::memo: Reformat benchmarking docs by @WiscEvan in https://github.com/KwanLab/Autometa/pull/215
  • Refactor autometa-taxonomy-lca by @WiscEvan in https://github.com/KwanLab/Autometa/pull/211
  • :art::whale: Replace jason-c-kwan with jasonkwan for docker images by @WiscEvan in https://github.com/KwanLab/Autometa/pull/217
  • Update mockdatareporter.Dockerfile by @chasemc in https://github.com/KwanLab/Autometa/pull/220
  • :whale::green_heart::memo: Add docker CI and update links by @WiscEvan in https://github.com/KwanLab/Autometa/pull/216
  • Simplify Licensing by @chasemc in https://github.com/KwanLab/Autometa/pull/222
  • Add check for nr.dmnd and nr.gz by @chasemc in https://github.com/KwanLab/Autometa/pull/221
  • 🍏 Change Nextflow I/O behavior by @WiscEvan in https://github.com/KwanLab/Autometa/pull/218
  • :green_apple::art: add/update coverage handling by @WiscEvan in https://github.com/KwanLab/Autometa/pull/223
  • :snake:🐎 Large data mode by @WiscEvan in https://github.com/KwanLab/Autometa/pull/207
  • Merge main into dev by @WiscEvan in https://github.com/KwanLab/Autometa/pull/224
  • pytest & codecov CI by @WiscEvan in https://github.com/KwanLab/Autometa/pull/227
  • Refactor samplesheet by @WiscEvan in https://github.com/KwanLab/Autometa/pull/228
  • 🐛 🎨 🍏 Fix kingdom-handling and mounting NCBI databases into docker container by @WiscEvan in https://github.com/KwanLab/Autometa/pull/229
  • Add error handling strategies for nextflow processes by @WiscEvan in https://github.com/KwanLab/Autometa/pull/231
  • Release 2.0.0 by @WiscEvan in https://github.com/KwanLab/Autometa/pull/233
  • :memo::art::arrow_up::fire: update build files and respective docs by @WiscEvan in https://github.com/KwanLab/Autometa/pull/234
  • Add badges and links to README.md by @WiscEvan in https://github.com/KwanLab/Autometa/pull/235
  • GH action: Add dynamic docker tags by @WiscEvan in https://github.com/KwanLab/Autometa/pull/236
  • Update nextflow-workflow.rst by @samche42 in https://github.com/KwanLab/Autometa/pull/238
  • :bug::fire: Fix bedtools coverage calculation bug by @WiscEvan in https://github.com/KwanLab/Autometa/pull/243

New Contributors

  • @chasemc made their first contribution in https://github.com/KwanLab/Autometa/pull/119
  • @samche42 made their first contribution in https://github.com/KwanLab/Autometa/pull/238

Full Changelog: https://github.com/KwanLab/Autometa/compare/1.0.3...2.0.1

- Python
Published by WiscEvan almost 4 years ago

autometa - 2.0.0

Full Changelog: https://github.com/KwanLab/Autometa/compare/2.0...2.0.0

- Python
Published by WiscEvan about 4 years ago

autometa - 1.0.3

  • 🐍 Deprecate python2.7 code
  • 🐳 🐛 Dockerfile fix

- Python
Published by WiscEvan over 4 years ago

autometa - 1.0.2

🐛 Now handles case where all contigs are clustered in the first DBSCAN round causing an empty table to be passed in the following round. This previously caused a ValueError resulting in the clustering not being written. Now the clustered contigs are written.

- Python
Published by WiscEvan over 5 years ago

autometa - 1.0.1

Bug fixes

  • Now processes NCBI merged.dmp to account for deprecated/suppressed taxids at taxonomy stages.
  • Removes the 2.7 shebangs so the user's specified python environment is used
  • Bug fix to nr.dmnd.md5 check

- Python
Published by WiscEvan over 5 years ago

autometa - Autometa v1.0

Release of Autometa Version 1.0

- Python
Published by WiscEvan about 6 years ago