Docstring:
Usage: qiime pepsirf subjoin [OPTIONS]
Manipulate matrix files with pepsirf's subjoin module
Inputs:
--i-multi-file ARTIFACT The name of a tab-delimited file containing score
MultiFile matrix and sample name list filename pairs, one per
line. Each of these pairs must be a score matrix and
a file containing the names of samples (or peptides,
if specified) to keep from the input the score
matrix. The score matrix should be of the format
output by the demux module, with sample names on the
columns and peptide names on the rows. The namelist
must have one name per line, but can optionally have
2, if renaming samples in the subjoin output.
Optionally, a name list can be omitted if all
samples from the input matrix should be included in
the output. [optional]
Parameters:
--p-input-type VALUE Str % Choices('raw')¹ | Str % Choices('col_sum')² |
Str % Choices('diff')³ | Str % Choices('diff_ratio')⁴ | Str %
Choices('ratio')⁵ | Str % Choices('size_factors')⁶
Specify the type of file being inputted into
subjoin, in order to produce the correct output file
format type. raw = FeatureTable[RawCounts], col_sum
= FeatureTable[Normed], etc. [default: 'raw']
--p-multi-file-input TEXT...
List[Str] To use multiple name lists with multiple score
matrices, include this argument with a list of file
names. Optionally, a name list can be omitted if all
samples from the input matrix should be included in
the output. Ex:(file1,file1_samples
file2,file2_samples) or Ex:(file1 file2 file3).
[optional]
--p-subjoin-input TEXT Comma-separated filenames (For example:
score_matrix.tsv,sample_names.txt ). Each of these
pairs must be a score matrix and a file containing
the names of samples (or peptides, if specified) to
keep in the score matrix. The score matrix should be
of the format output by the demux module, with
sample names on the columns and peptide names on the
rows. The namelist must have one name per line, but
can optionally have 2. If 2 tab-delimited names are
included on one line, the name in the first column
should match the name in the input matrix file,
while the name in the second column will be output.
Therefore, this allows for the renaming of samples
in the output. [optional]
--p-filter-peptide-names / --p-no-filter-peptide-names
Flag to include if the name lists input to the
input or multi-file options should be treated as
peptide (i.e. row) names instead of sample (i.e.
column) names. With the inclusion of this flag, the
input files will be filtered on peptide names (rows)
instead of sample names (column). [default: False]
--p-duplicate-evaluation TEXT Choices('include', 'combine', 'ignore')
Defines what should be done when sample or peptide
names are not unique across files being joined.
Currently, three different duplicate evaluation
strategies are available: - combine: Combine (with
addition) the values associated with identical
sample/peptide names from different files. -
include: Include each duplicate, adding a suffix to
the duplicate name detailing the file from which the
sample came. - ignore: Ignore the possibility of
duplicates. Behavior is undefined when duplicates
are encountered in this mode Therefore, this mode
is not recommended. [default: 'include']
--p-outfile TEXT The outfile that will produce a list of inputs to
PepSIRF. [default: './subjoin.out']
--p-pepsirf-binary TEXT The binary to call pepsirf on your system.
[default: 'pepsirf']
Outputs:
--o-subjoin-output ARTIFACT FeatureTable[RawCounts¹ | Normed² |
NormedDifference³ | NormedDiffRatio⁴ | NormedRatio⁵ | NormedSized⁶]
Name for the output score matrix file. The output
will be in the form of the input, but with only the
specified values (samplenames or peptides) found in
the namelists. [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 subjoin
Docstring:
pepsirf subjoin module
Manipulate matrix files with pepsirf's subjoin module
Parameters
----------
input_type : Str % Choices('raw')¹ | Str % Choices('col_sum')² | Str % Choices('diff')³ | Str % Choices('diff_ratio')⁴ | Str % Choices('ratio')⁵ | Str % Choices('size_factors')⁶, optional
Specify the type of file being inputted into subjoin, in order to
produce the correct output file format type. raw =
FeatureTable[RawCounts], col_sum = FeatureTable[Normed], etc.
multi_file_input : List[Str], optional
To use multiple name lists with multiple score matrices, include this
argument with a list of file names. Optionally, a name list can be
omitted if all samples from the input matrix should be included in the
output. Ex:(file1,file1_samples file2,file2_samples) or Ex:(file1 file2
file3).
multi_file : MultiFile, optional
The name of a tab-delimited file containing score matrix and sample
name list filename pairs, one per line. Each of these pairs must be a
score matrix and a file containing the names of samples (or peptides,
if specified) to keep from the input the score matrix. The score matrix
should be of the format output by the demux module, with sample names
on the columns and peptide names on the rows. The namelist must have
one name per line, but can optionally have 2, if renaming samples in
the subjoin output. Optionally, a name list can be omitted if all
samples from the input matrix should be included in the output.
subjoin_input : Str, optional
Comma-separated filenames (For example:
score_matrix.tsv,sample_names.txt ). Each of these pairs must be a
score matrix and a file containing the names of samples (or peptides,
if specified) to keep in the score matrix. The score matrix should be
of the format output by the demux module, with sample names on the
columns and peptide names on the rows. The namelist must have one name
per line, but can optionally have 2. If 2 tab-delimited names are
included on one line, the name in the first column should match the
name in the input matrix file, while the name in the second column will
be output. Therefore, this allows for the renaming of samples in the
output.
filter_peptide_names : Bool, optional
Flag to include if the name lists input to the input or multi_file
options should be treated as peptide (i.e. row) names instead of sample
(i.e. column) names. With the inclusion of this flag, the input files
will be filtered on peptide names (rows) instead of sample names
(column).
duplicate_evaluation : Str % Choices('include', 'combine', 'ignore'), optional
Defines what should be done when sample or peptide names are not unique
across files being joined. Currently, three different duplicate
evaluation strategies are available: - combine: Combine (with addition)
the values associated with identical sample/peptide names from
different files. - include: Include each duplicate, adding a suffix to
the duplicate name detailing the file from which the sample came. -
ignore: Ignore the possibility of duplicates. Behavior is undefined
when duplicates are encountered in this mode Therefore, this mode is
not recommended.
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
-------
subjoin_output : FeatureTable[RawCounts¹ | Normed² | NormedDifference³ | NormedDiffRatio⁴ | NormedRatio⁵ | NormedSized⁶]
Name for the output score matrix file. The output will be in the form
of the input, but with only the specified values (samplenames or
peptides) found in the namelists.
