pyorthoani - v0.7.0

Changed

• Rename orthoani to pyorthoani.
• Use pyproject.toml instead of setup.py to handle project with setuptools.

- Python
Published by github-actions[bot] about 1 year ago

pyorthoani - v0.6.0

Changed

• Make better-exceptions an optional dependency. ### Fixed
• Discrepancy with OrthoANI values for high similarity genomes (#2).
• Remaining files of temporary BLAST databases not being removed. ### Removed
• Support for Python 3.5.

- Python
Published by github-actions[bot] over 1 year ago

pyorthoani - 0.5.0

Fixed

• Exception messages not properly rendering with --traceback enabled.
• Use os.cpu_count instead of multiprocessing.cpu_count where applicable.
• Make BlockIterator zero-copy using indices instead of slices. ### Changed
• Use seqidlist to reduce number of blocks compared in backward search.
• Switch to use BLASTdb v5 (instead of v4 previously).
• Prefix temporary files with orthoani prefix.
• Skip blocks containing more than 80% unknown nucleotides like in original implementation.
• Average ANI values based on HSPs instead of reciprocical blocks like in original implementation.

- Python
Published by althonos over 4 years ago

pyorthoani - 0.4.0

Changed

• Entire sequences smaller than the given blocksize will be padded with N.
• biopython requirement was relaxed to v1.73. ### Fixed
• Code using builtin API not available in Python3.5.

- Python
Published by althonos over 5 years ago

pyorthoani - 0.3.2

Fixed

• orthoani CLI ignoring the value of the --jobs flag.

- Python
Published by althonos over 5 years ago

pyorthoani - 0.3.1

Fixed

• blastn and makeblastdb being called with shell=True, causing issues if shell cannot be forked.
• Traceback not being displayed even with --traceback flag. ### Changed
• ANI values are collected using decimal.Decimal instead of float.

- Python
Published by althonos over 5 years ago

pyorthoani - 0.3.0

Added

• Support for genomes segmented in multiple contigs.

- Python
Published by althonos over 5 years ago

pyorthoani - 0.2.1

Fixed

• Temporary files with chopped FASTA not being deleted.

- Python
Published by althonos over 5 years ago

pyorthoani - 0.2.0

Added

• threads argument controlling BLASTn thread count to orthoani and orthoani_pairwise.
• -j / --jobs flag controlling BLASTn thread count to CLI.
• Proper documentation and error codes to CLI.
• orthoani console script to call the CLI without python -m invocation.

- Python
Published by althonos over 5 years ago

pyorthoani - 0.1.0-post1

Fixed

• Travis-CI badge not rendering on README.md. ### Changed
• Made development status Beta instead of Alpha in setup.cfg.

- Python
Published by althonos over 5 years ago

pyorthoani - 0.1.0

Initial release.

- Python
Published by althonos over 5 years ago