Changelogs » Metawibele

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Metawibele

0.3.7

* Added functions for downloading databases
  * Added binary filtering for unsupervised prioritization
  * Added config for interproscan executable file

0.3.6

* Make input/output options available for metawibele on the command line instead of the config file
  * Add options for dependent files for each individual step
  * Report all DDIs and microbe-human DDIs
  * Fixed errors when running DDI-based annotations

0.3.5

* Skip phenotypic association by default
  * Skip supervised prioritization if not associating with environmental/phenotypic parameters
  * Turn off input/output options in workflows and only use info from the configuration file

0.3.4

* Update DDIs which are supported by PDB
  * Update default settings of Maaslin2
  * Update function to build dependent databases
  * Set cases where running DDIs without domain annotations
  * Add bypass modes for each individual domain/motif annotation step
  * Rename finalized taxonomic annotation file

0.3.3

* Add utilities to build dependent uniref and domain databases
  * Simplify the configurations in metawibele.cfg
  * Deprecate sample_list and gene_catalog configs in metawibele.cfg
  * Replace 'metawibele_workflow' with 'metawibele'
  * Update configuration of depedent databases

0.3.2

* Use UniRef/UniProt databases in HUMAnN
  * Remove to map assembled proteins to UniRef50
  * Pack default dependent databases: domain databases, taxonomy databases
  * Add function to download gloabl and local configuration files
  * Remove specific utility scripts in the common folder
  * Add option for readling compressed databases
  * Balance gridable tasks
  * Add option to preprocess outputs from only prokka, only prodigal, or both

0.3.1

* Convert input sources for gridable task
  * Reformat annotations of PSORTb, InterProScan
  * Add EffectiveT3 to predict effector (TBD)
  * Make config file for MSPminer as optional

0.3

* Update different cases for binary filtering
  * Update local and global configuration files
  * Add Rscripts folder

0.2.2

* Update binary filtering approaches for supervised prioritization

0.2.1

* Add setup.py

0.2

* Add preprocessing workflow
  * Update linear models for association analysis
  * Modify abundance features

0.1

* Initial characterization and prioritization processing workflows added