https://github.com/bactopia/bactopia-py - v1.6.1

1.6.1

• shuffle ncbi related module out of utils and into ncbi
• fixed missing import in bactopia-prepare

- Python
Published by rpetit3 9 months ago

https://github.com/bactopia/bactopia-py - v1.6.0

1.6.0

• bactopia-search
  • fixed issue when no tax id is associated with an accession
  • NCBI genome size is now optional (--use-ncbi-genome-size)
  • moved modules to specific database files
• Remove executor dependency

- Python
Published by rpetit3 9 months ago

https://github.com/bactopia/bactopia-py - v1.5.1

1.5.1

• fix ena metadata parsing in bactopia-search to handle missing columns

- Python
Published by rpetit3 9 months ago

https://github.com/bactopia/bactopia-py - v1.5.0

1.5.0

• actually remove --force from mamba|conda commands

- Python
Published by rpetit3 about 1 year ago

https://github.com/bactopia/bactopia-py - v1.4.0

1.4.0

• added:
  • bactopia-pubmlst-setup to setup PubMLST REST API connections
  • bactopia-pubmlst-build to build PubMLST databases compatible with mlst Bactopia Tool

- Python
Published by rpetit3 about 1 year ago

https://github.com/bactopia/bactopia-py - v1.3.0

1.3.0

• replace conda/mamba --force with simple rm -rf
  • latest version of mamba removed --force

- Python
Published by rpetit3 over 1 year ago

https://github.com/bactopia/bactopia-py - v1.2.1

1.2.1

• added parallel gzipping of assemblies in bactopia-atb-formatter
• added size estimation to bactopia-atb-formatter output

- Python
Published by rpetit3 over 1 year ago

https://github.com/bactopia/bactopia-py - v1.2.0

1.2.0

• added bactopia-atb-downloader to download All-the-Bacteria assemblies

- Python
Published by rpetit3 over 1 year ago

https://github.com/bactopia/bactopia-py - v1.1.1

1.1.1

• fixed bactopia-summary not working with Bakta annotations
• added support for alternative extensions in bactopia-atb-formatter @nickjhathaway 🎉

- Python
Published by rpetit3 almost 2 years ago

https://github.com/bactopia/bactopia-py - v1.10.0

1.10.0

• rework bactopia-summary for new AMRFinder+ outputs

- Python
Published by rpetit3 almost 2 years ago

https://github.com/bactopia/bactopia-py - v1.0.9

1.0.9

• added bactopia-atb-formatter to format All-the-Bacteria assemblies for Bactopia

- Python
Published by rpetit3 about 2 years ago

https://github.com/bactopia/bactopia-py - v1.0.8

1.0.8

• Fixed bactopia-prepare usage of --prefix not working

- Python
Published by rpetit3 over 2 years ago

https://github.com/bactopia/bactopia-py - v1.0.7

1.0.7

• Fixed bactopia-search not including header name in accessions.txt
• Added --hybrid and --short-polish to bactopia-prepare

- Python
Published by rpetit3 over 2 years ago

https://github.com/bactopia/bactopia-py - v1.0.6

1.0.6

• Fixed bactopia-summary handling of empty searches

- Python
Published by rpetit3 over 2 years ago

https://github.com/bactopia/bactopia-py - v1.0.5

1.0.5

• Fixed bactopia-download not building prokka and bakta conda envs

- Python
Published by rpetit3 over 2 years ago

https://github.com/bactopia/bactopia-py - v1.0.4

1.0.4

• Fixed bactopia-summary working with new output structure

- Python
Published by rpetit3 almost 3 years ago

https://github.com/bactopia/bactopia-py - v1.0.3

1.0.3

• Fixed bactopia-search using missing columns in the query
• dropped pysradb dependency

- Python
Published by rpetit3 almost 3 years ago

https://github.com/bactopia/bactopia-py - v1.0.2

1.0.2

• Added bactopia-datasets to download optional datasets outside of Nextflow
• consistently use --bactopia-path across sub-commands

- Python
Published by rpetit3 almost 3 years ago

https://github.com/bactopia/bactopia-py - v1.0.1

1.0.1

Renamed parameter --bactopia to --bactopia-path in bactopia-download

- Python
Published by rpetit3 about 3 years ago

https://github.com/bactopia/bactopia-py - v1.0.0

1.0.0

Initial release of the bactopia-py package. This release ports the Python helper scripts from the main Bactopia repo.

- Python
Published by rpetit3 about 3 years ago