- Replace urease with seqkit
- Refine config of reference
- Refine prepare_uniprot_taxonomy function
- Updated prepare_uniprot_annotation
- Tweake gene_abundance function
- Add threads parameter for indexing database
- Added more parallel option for preprocessing workflow
- Tweaked uniref_protein function to save memory
- Added function to handle outputs of MSPminer >v1.0.0
- Printed the contents of the variable mysterr for debugging the dependency installs
- The fixed version has been tagged v0.4.6
- Tweaked task names for the preprocessing workflow
- Fixed issue when running gridable jobs with one local job
- Updated publication information
- The fixed version has been tagged v0.4.5
- Release v0.4.4
- Updated URLs of dependencies
- Added case when skipping mspminer-based taxonomic assignment
- Release v0.4.3
- Fixed maaslin2 incompatibility
- Release new version
- Fixed small issue on psortb annotator
- Cut down some space of demo data
- Fixed issues when running interproscan with all analyses
- Updated requirements for install
- Added a new module to check install
- Fixed issue when running utilities to prepare databases
- Fixed issue in config annotation types from interproscan
- Keep temp directory
- Updated description texts about configs
- Added final taxonomy file with stratified taxon info
- Fixed small issue in utilities
- Added "--tshld-diff" "--tshld-classified" setting to global config file
- Added "--min_variance" "--reference" for MaAsLin2 >= v1.5.1
- Added "--global-config" option for taking the user provided global config file
- Added time stamp for each processing step
- Added default setting for uniref database and mutiple options for setting up the DB
- Added option for downloading demo database
- Added options for msp-based taxonomy assignment "--tshld-diff" "--tshld-classified"
- Renamed the name of config option for taxonomy assignment
- Fixed option setting for interproscan
- Added option for FDR correction
- Fixed issue when preprocessing contigs
- Fixed warnings when summarizing interproscan output
- Added bowtie2 options "--very-sensitive"
- Fixed issue of summarizing uniref annotations and contig sequences
- Added functions for downloading databases
- Added binary filtering for unsupervised prioritization
- Added config for interproscan executable file
- Fixed issue when formatting assembled protein sequences
- 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
- 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
- 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
- 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
- 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
- Convert input sources for gridable task
- Reformat annotations of PSORTb, InterProScan
- Add EffectiveT3 to predict effector (TBD)
- Make config file for MSPminer as optional
- Update different cases for binary filtering
- Update local and global configuration files
- Add Rscripts folder
- Update binary filtering approaches for supervised prioritization
- Add setup.py
- Add preprocessing workflow
- Update linear models for association analysis
- Modify abundance features
- Initial characterization and prioritization processing workflows added