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OBITools3
Last edited by Celine Mercier
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Updating and release notes

Current version: 3.0.0b20

You can check the version installed by running obi --version

Release notes:

  • 3.0.0b20: Reworked the installation (and version formatting) to work with pip, and made obi import work with seq genbank extension (+ other minor import fixes).

  • 3.0.0-beta17: Fixed a bug in obi import stopping the program when the last line of a fasta file contained a single nucleotide.

  • 3.0.0-beta16: Fixed the import and dereplication of old obitools files containing premerged informations, and other minor improvements.

  • 3.0.0-beta15: Various fixes and improvements, including notable bugs in ecotag and build_ref_db that made ecotag less specific than it should have been.

  • 3.0.0-beta14:

    • Fixed a memory bug when importing a taxdump and building the list of merged taxids
    • Improved disk space management when filling columns

  • 3.0.0-beta13:

    • obi import: fixed a critical bug where the last entry of embl and genbank files was not imported.

    • ecopcr now prints a warning instead of stopping when not finding a taxid.

    • Various other small bug fixes, and improvements in documentation, error messages and checks.

  • 3.0.0-beta11: Fixed a bug in obi cat when concatenating views with columns having different key sets, and a bug in obi ecotag generating badly formatted column comments.

  • 3.0.0-beta10: obi import: new option --preread to do a first readthrough of the dataset if it contains huge dictionaries for a much faster import.

  • 3.0.0-beta9: Better disk space management when importing files (rewritten columns are deleted).

  • 3.0.0-beta8: Fixed a bug when importing a file where the first entry would contain a dictionary with a single key.

  • 3.0.0-beta7: Added the 'obi' prefix in the bash history commands, and fixed a compilation issue with some versions of gcc.

  • 3.0.0-beta6: New command: obi cat to concatenate views, and various inconsequential fixes.

  • 3.0.0-beta5: Fixed a bug in ngsfilter when there is only one tag.

  • 3.0.0-beta4: Fixed and improved the options to keep nucleotides around the amplicon in ecopcr.

  • 3.0.0-beta3: Fixed bugs in ngsfilter when cutting sequences, and a few minor bugs.

How to update with pip:

From the OBITools3 virtual environment, run:

pip3 install --pre --upgrade OBITools3

How to update with git:

From the OBITools3 installation directory and virtual environment, run:

git pull
python3 setup.py install