Docstring:
Usage: qiime pepsirf enrich [OPTIONS]
Determines which peptides are enriched in samples with pepsirf's enrich
module
Inputs:
--i-thresh-file ARTIFACT
EnrichThresh The name of a tab-delimited file containing one
tab-delimited matrix filename and threshold(s), one
per line. If providing more than z score matrix.
[optional]
--i-zscores ARTIFACT FeatureTable[Zscore]
FeatureTable containing z scores of the normalized
read counts. Fist column header must be 'Sequence
Name' as produced by pepsirf. [optional]
--i-col-sum ARTIFACT FeatureTable[Normed]
FeatureTable containing the normalized read counts.
Fist column header must be 'Sequence Name' as produced
by pepsirf. [optional]
--i-raw-scores ARTIFACT FeatureTable[RawCounts]
This matrix must contain the raw counts for each
Peptide for every sample of interest. If included,
'--raw_score_constraint' must also be specified.
[optional]
Parameters:
--m-source-file METADATA
--m-source-column COLUMN MetadataColumn[Categorical]
Metadata file containing all sample names and their
source groups. Used to create pairs tsv to run pepsirf
enrich module. [required]
--p-flex-reps / --p-no-flex-reps
[default: False]
--p-exact-z-thresh TEXT
Exact z score thresholds. [optional]
--p-exact-cs-thresh TEXT
Exact col-sum threholds. [optional]
--p-raw-constraint INTEGER
Range(0, None) The minimum total raw count across all peptides for a
sample to be included in the analysis.This provides a
way to impose a minimum read count for a sample to be
evaluated. [optional]
--p-enrichment-failure / --p-no-enrichment-failure
For each sample set that does not result in the
generation of an enriched peptide file, a row of two
tab-delimited columns is provided: the first column
contains the replicate names (comma-delimited) and the
second column provides the reason why the sample did
not result in an enriched peptide file. This file is
output to the same directory as the enriched peptide
files. The 'Reason' column will contain one of the
following: 'Raw read count threshold' or 'No enriched
peptides'. [default: False]
--p-truncate / --p-no-truncate
By default each filename in the output directory will
include every replicate name joined by the 'join_on'
value. Alternatively, if more than two replicates are
being evaluated, then you may include this flag to
stop the filenames from including more than 3
samplenames in the output. When this flag is used, the
output names will be of the form 'A~B~C~1more', for
example. [default: False]
--p-outfile TEXT The outfile that will produce a list of inputs to
PepSIRF. [default: './enrich.out']
--p-pepsirf-binary TEXT
The binary to call pepsirf on your system.
[default: 'pepsirf']
Outputs:
--o-dir-fmt-output ARTIFACT
PairwiseEnrichment Directory formatted qza containing lists of enriched
peptides [required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr during
execution of this action. Or silence output if
execution is successful (silence is golden).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Import:
from qiime2.plugins.pepsirf.methods import enrich
Docstring:
pepsirf enrich module
Determines which peptides are enriched in samples with pepsirf's enrich
module
Parameters
----------
source : MetadataColumn[Categorical]
Metadata file containing all sample names and their source groups. Used
to create pairs tsv to run pepsirf enrich module.
flex_reps : Bool, optional
thresh_file : EnrichThresh, optional
The name of a tab-delimited file containing one tab-delimited matrix
filename and threshold(s), one per line. If providing more than z score
matrix.
zscores : FeatureTable[Zscore], optional
FeatureTable containing z scores of the normalized read counts. Fist
column header must be 'Sequence Name' as produced by pepsirf.
col_sum : FeatureTable[Normed], optional
FeatureTable containing the normalized read counts. Fist column header
must be 'Sequence Name' as produced by pepsirf.
exact_z_thresh : Str, optional
Exact z score thresholds.
exact_cs_thresh : Str, optional
Exact col-sum threholds.
raw_scores : FeatureTable[RawCounts], optional
This matrix must contain the raw counts for each Peptide for every
sample of interest. If included, '--raw_score_constraint' must also be
specified.
raw_constraint : Int % Range(0, None), optional
The minimum total raw count across all peptides for a sample to be
included in the analysis.This provides a way to impose a minimum read
count for a sample to be evaluated.
enrichment_failure : Bool, optional
For each sample set that does not result in the generation of an
enriched peptide file, a row of two tab-delimited columns is provided:
the first column contains the replicate names (comma-delimited) and the
second column provides the reason why the sample did not result in an
enriched peptide file. This file is output to the same directory as the
enriched peptide files. The 'Reason' column will contain one of the
following: 'Raw read count threshold' or 'No enriched peptides'.
truncate : Bool, optional
By default each filename in the output directory will include every
replicate name joined by the 'join_on' value. Alternatively, if more
than two replicates are being evaluated, then you may include this flag
to stop the filenames from including more than 3 samplenames in the
output. When this flag is used, the output names will be of the form
'A~B~C~1more', for example.
outfile : Str, optional
The outfile that will produce a list of inputs to PepSIRF.
pepsirf_binary : Str, optional
The binary to call pepsirf on your system.
Returns
-------
dir_fmt_output : PairwiseEnrichment
Directory formatted qza containing lists of enriched peptides
