Amalgkit 0.6.0.0 changelog

[Hego-CCTB]

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.

[Hego-CCTB]

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]

Is there any option like --curate_group all to include all curate_group in the metadata table?

[Hego-CCTB]

If --curate_group is left none , it should parse out all unique values from the curate_group column and use that as input.

[kfuku52]

Sounds good!

[Hego-CCTB]

Update is now live.
cbd6852

[kfuku52]

The curate_group column is missing in the metadata table. Could you update amalgkit metadata?

[Hego-CCTB]

Ah, it seems the column doesn't survive the last metadata step. There are 3 metadata sheets as output. curate_group is in the second output, but not in the third.

I'll investigate that.

[kfuku52]

It seems that curate_group isn't used at all in transcriptome_curation.r. Am I missing something?

[Hego-CCTB]

Yeah, you are right. I'm gonna need to replace any reference to tissue with curate_group.

[Hego-CCTB]

Yeah, you are right. I'm gonna need to replace any reference to tissue with curate_group.

Amalgkit ver. 0.6.2.3

• Replaced every 'tissue' or 'tissues' with 'curate_group' or 'curate_groups', including variables
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