GitLab

Current version: 3.0.0b28

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

Release notes:

• 3.0.0b28:

• all commands: now handle output to buffer object (e.g. stdout)
• ngsfilter: unidentified sequences are now kept untrimmed
• alignpairedend: improved/fixed the output tags for the alignment score and lengths
• grep: now prints the number of entries grepped

• 3.0.0b27:

  • uniq: fixed a bug where some sequences were not properly dereplicated
  • clean: fixed the behaviour when no or bad sample information is given

• 3.0.0b26:

  • export: dictionaries are now formatted as they were in the original OBITools, and fixed tuple formatting
  • ngsfilter: reversed tag is now set to 'False' instead of 'None' when false.

• 3.0.0b25:

  • ls: fixed an issue with big DMS
  • ngsfilter: made one of the tag error messages more accurate ('No tags found' changed to 'No sample with that tag combination')
  • grep and uniq now output empty views when the input is an empty view

• 3.0.0b24:

  • Improved ecotag output with list of taxids of best matches
  • Improved uniq progress bar
  • Fixed bash history display for views
  • Fixed bugs with the output of sequences unaligned ('joined') by alignpairedend
  • Fixed a bug where tuple columns would 'lose' their indexer in some cases

• 3.0.0b23: Fixed installation on Ubuntu without pip (problem introduced in 3.0.0b20).

• 3.0.0b22: Fixed a bug when skipping unreadable sequences in obi import.

• 3.0.0b21: Improved import of Genbank seq files.

• 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