v2.6.3

Some updates:

• Added a check for empty trait tables: this was specifically an issue if users created custom trait tables and these were empty/summed to zero for one of the domains
• PFAM names were updated: in the PICRUSt2-SC database these used the names given by Eggnog as annotations. These have now been mapped to PFAM ID's (where possible) so that they match the description map files. The add_descriptions script can now be used with the PFAM ID's again. Note that there were a few PFAM names from the Eggnog annotations that didn't have PFAM ID's; these have been left as they are but they have no additional descriptions.
• Script naming for the scripts that work with only a single domain, rather than the PICRUSt2-SC separate reference files for bacteria and archaea, has been updated. This reflects that these scripts aren't only for use with the oldIMG database, but can be for fungi, either/or of the bacteria/archaea files, another custom database, etc.

What's Changed

• Picrust2-v2.6.3 by @R-Wright-1 in #399
  Full Changelog: v2.6.2...v2.6.3

v2.6.2

Minor changes mainly updating version name, database name (from MPGA to SC).
There seemed to be issues with installing from conda in v2.6.1 where the bacteria and archaea folders within default_files don't get downloaded, so hoping this will fix that, too.

Full Changelog: v2.6.1...v2.6.2

v2.6.1-pub

Release created for purpose of Zenodo archiving with publication of Application Note for updated PICRUSt2 database.

v2.6.1

What's Changed

• Fix picrust2-env.yaml dependencies by @whatever60 in #378
• Fix default map file for Metacyc pathways

Full Changelog: v2.6.0...v2.6.1

PICRUSt2 v2.6.0

Summary:

• Updating to PICRUSt2-v2.6.0 to work with new PICRUSt2-MPGA database. Please see Wiki page for full details.
• New PICRUSt2-MPGA database contains separate reference files and annotations for bacteria and archaea.
• New default workflow:
  • Previous place sequences step is split to placing in bacterial and archaeal reference trees by default.
  • Hidden state prediction is run separately for 16S for bacteria and archaea to determine NSTI for all sequences for both reference sets. The best-fitting domain for each sequence is then chosen (based on lowest NSTI) and the files are filtered to contain only those that fit the best.
  • Hidden state prediction is then run for KOs and EC numbers for both bacteria and archaea.
  • Combine bacterial and archaeal predictions for KOs and EC numbers.
• Closest reference genome is now given for all sequences.
• Added ete3 requirement.
• Changed several dependency versions, hoping this will fix issues for some Mac users

What's Changed

• PICRUSt2-v2.6.0 by @R-Wright-1 in #372

New Contributors

• @R-Wright-1 made their first contribution in #372

Full Changelog: v2.5.3...v2.6.0

PICRUSt2 v2.5.3

Minor compatibility changes:

• Add file for editable pip install to continue working
• Addressed pandas deprecation warnings
• Change dependencies to be compatible with latest QIIME 2 environment (including latest SEPP and specifying version of dendropy that is compatible).

PICRUSt2 v2.5.2

• Fixed dtype warning issue reported here (Note that this did not seem to affect the output either way)

• Changed lower bound for h5py to enable compatibility with QIIME 2 conda environment (and also enable glpk and r-castor to be compatible with higher versions)

• flake8-identified formatting cleanups

• Cleaned-up redundant info and version info across files (specifically, just list version number, license, etc., in setup.pyrather than in all files)

• Removed unnecessary script print_picrust2_config.py

PICRUSt2 v2.5.1

Fixed incompatibility issues related to newer versions of dependencies, specifically numpy and pandas.

PICRUSt2 v2.5.0

• Fixed important bug where the "norm_taxon_function_contrib" column of the contrib (i.e., stratified) output tables contained wrong values (e.g., #206). This was especially clear from the fact that the values were frequently NA or > 1 (when they should all be proportional). Many thanks to @ragavishn and Vincent Darbot for bringing this to my attention.

• Added several checks to input sequence abundance table (especially when it is provided as a simple TSV table). This should provide more informative error messages regarding how the table is malformed and how it can be fixed.

• Added check for whitespace in input FASTA file headers to provide informative message (otherwise this often results in issues with hmmalign / placement workflow that isn't obvious from the errors)

• Bumped versions of gappa and castor dependencies to latest versions.

• Added "cython" as a dependency to avoid installation problems (thanks @crusher083!)

PICRUSt2 v2.4.2

Minor update, primarily to add functionality with Python 3.8. Also now tests are run with Circle CI instead of Travis CI.