Hego-CCTB
commented
3 years ago Changelog Amalgkit ver. 0.6.0.0
amalgkit csca
- new sub function for cross species correlation analysis
- USAGE:
amalgkit csca \ --out_dir \ PATH_TO_WORKING_DIRECTORY \ --file_species_tree \ PATH_TO_NWK_FILE \ --file_singlecopy \ PATH_TO_ORTHOFINDER_FILE \ --file_orthogroup \ PATH_TO_ORTHOFINDER_FILE \ --dir_uncorrected_curate_group_mean \ PATH_TO_CURATE_TABLES\ --dir_curate_group_mean\ PATH_TO_CURATE_TABLES\ --dir_sra \ PATH_TO_CURATE_TABLES\ --dir_tc \ PATH_TO_CURATE_TABLES\
--curate_group \ 'root,flower,leaf' \
- Note: This was tested on a 9 species plant dataset retrieved, quantified and curated by `amalgkit`. That said, further testing is needed. Especially gene name format can cause issues.
- Note: `dir_uncorrected_curate_group_mean`, `dir_curate_group_mean`, `dir_sra`, `dir_tc` all point to the same directory, if the input is unchanged `curate` output. As such, these arguments are `inferred` by default. If there is a `curate/tables` folder in the `--out_dir` path, amalgkit will find those files on its own.
## `amalgkit curate`
- Now throws a warning when transforming with TPM
- Now throws an error when `cstmm` output files are detected (parsed from path) in combination with TPM transformation
- Now includes option `--one_outlier_per_iter yes|no`, which allows only 1 sample per same bioproject or same tissue to be removed per iteration of the outlier removal
- `check_within_tissue_correlation()` now removes samples below a pearson r of 0.2 (currently hard coded, but can be made an optional input in the future)
- `--cleanup 0|1` is now `plot_intermediate yes|no`. "yes" calculates and prints SVA correction after every single iteration of outlier removal. This can drastically increase runtimes.
## `amalgkit getfastq`
- truncated updated_metadata output files to only essential columns for `curate`. This comes with two benefits: lower filesize (which very slightly increases `curate` performance) and more importantly, same column number across all individual files
- obsoleted `--ascp` and all related options
## `amalgkit`
- added `amalgkit csca` subparsers
This should go up later today. I'm still debugging and I have to merge with the other updates today.
kfuku52
This is going to be a bigger update, affecting multiple currently open issues. So I'll post the changelog in here and refer to this from the other issues.