Comments (10)
Yeah, you are right. I'm gonna need to replace any reference to tissue with curate_group.
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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 unchangedcurate
output. As such, these arguments areinferred
by default. If there is acurate/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 nowplot_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 increasescurate
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.
from amalgkit.
Is there any option like --curate_group all
to include all curate_group in the metadata table?
from amalgkit.
If --curate_group
is left none
, it should parse out all unique values from the curate_group column and use that as input.
from amalgkit.
Sounds good!
from amalgkit.
Update is now live.
cbd6852
from amalgkit.
The curate_group
column is missing in the metadata table. Could you update amalgkit metadata
?
from amalgkit.
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.
from amalgkit.
It seems that curate_group
isn't used at all in transcriptome_curation.r
. Am I missing something?
from amalgkit.
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
2174567
from amalgkit.
Related Issues (20)
- is_unpaird_file --> is_unpaired_file? HOT 1
- print('layout = {}; Deleting unpaired file: {}'.format(sra_stat['layout'], unpaired_file)) NameError: name 'unpaired_file' is not defined HOT 3
- getfastq OSError: [Errno 5] Input/output error: HOT 1
- amalgkit getfastq on folder with already-processed samples is re-running HOT 13
- merge plot HOT 1
- mapping rate and cstmm factor in the curate SV predictive power plot HOT 1
- use seqkit instead of pigz to compress fastq
- Effect of negative value clipping in log(x+1) values HOT 1
- FutureWarning: The argument 'infer_datetime_format' is deprecated and will be removed in a future version. HOT 1
- ValueError: No objects to concatenate
- amalgkit curate --h HOT 1
- Obsoleting search_term_*.config HOT 3
- Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
- Code for rRNA rate HOT 2
- Error in if (child1_color == child2_color) { :
- Output uncorrected tables without going through all of curate HOT 3
- cstmm - curate incompatibility HOT 4
- Metadata example command HOT 3
- Duplication rate and insert size peak from the fastp json report
- curate_group -> sample_group HOT 3
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