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Picrust2-v2.6.3#399

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R-Wright-1 merged 5 commits intomasterfrom
PICRUSt2-v2.6.3
Nov 27, 2025
Merged

Picrust2-v2.6.3#399
R-Wright-1 merged 5 commits intomasterfrom
PICRUSt2-v2.6.3

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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.

Update script naming from oldIMG to singleRef where appropriate, because this is still what would be used for a single reference e.g. for ITS. The oldIMG naming has been kept where the script is specific to the default IMG files used for prokaryotes.
Update from the PFAM names that Eggnog gave to PFAM ID's that were in previous versions and match the descriptions file
@R-Wright-1 R-Wright-1 merged commit b41a237 into master Nov 27, 2025
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@R-Wright-1 R-Wright-1 deleted the PICRUSt2-v2.6.3 branch November 27, 2025 15:39
cmorganl added a commit to Koonkie-Cloud-Services/picrust2-sc that referenced this pull request Jan 29, 2026
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