Docstring:
Usage: qiime pepsirf link [OPTIONS]
Defines linkages between taxonomic groups and peptides based on shared kmers
with pepsirf's link module
Inputs:
--i-protein-file ARTIFACT
ProteinFasta Name of fasta file containing protein sequences of
interest. [required]
--i-peptide-file ARTIFACT
PeptideFasta Name of fasta file containing aa peptides of
interest. These will generally be peptides that are
contained in a particular assay. [required]
Parameters:
--p-meta TEXT Optional method for providing taxonomic information
for each protein contained in '--protein-file'. Three
comma-separated strings should be provided: 1) name
of tab-delimited metadata file, 2) header for column
containing protein sequence name and 3) header for
column containing ID to be used in creating the
linkage map. [required]
--p-kmer-size INTEGER Kmer size to use when creating the linkage map.
[required]
--p-kmer-redundancy-control / --p-no-kmer-redundancy-control
Optional modification to the way scores are
calculated. If this flag is used, then instead of a
peptide receiving one point for each kmer it shares
with proteins of a given taxonomic group, it receives
1 / ( the number of times the kmer appears in the
provided peptides ) points. [default: False]
--p-outfile TEXT The outfile that will produce a list of inputs to
PepSIRF. [default: './link.out']
--p-pepsirf-binary TEXT
The binary to call pepsirf on your system.
[default: 'pepsirf']
Outputs:
--o-link-output ARTIFACT
Link Name of the file to which output is written. Output
will be in the form of a tab-delimited file with a
header. Each entry/row will be of the form:
peptide_name TAB id:score,id:score, and so on. By
default, 'score' is defined as the number of shared
kmers. [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 link
Docstring:
pepsirf link module
Defines linkages between taxonomic groups and peptides based on shared
kmers with pepsirf's link module
Parameters
----------
protein_file : ProteinFasta
Name of fasta file containing protein sequences of interest.
peptide_file : PeptideFasta
Name of fasta file containing aa peptides of interest. These will
generally be peptides that are contained in a particular assay.
meta : Str
Optional method for providing taxonomic information for each protein
contained in '--protein_file'. Three comma-separated strings should be
provided: 1) name of tab-delimited metadata file, 2) header for column
containing protein sequence name and 3) header for column containing ID
to be used in creating the linkage map.
kmer_size : Int
Kmer size to use when creating the linkage map.
kmer_redundancy_control : Bool, optional
Optional modification to the way scores are calculated. If this flag is
used, then instead of a peptide receiving one point for each kmer it
shares with proteins of a given taxonomic group, it receives 1 / ( the
number of times the kmer appears in the provided peptides ) points.
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
-------
link_output : Link
Name of the file to which output is written. Output will be in the form
of a tab-delimited file with a header. Each entry/row will be of the
form: peptide_name TAB id:score,id:score, and so on. By default,
'score' is defined as the number of shared kmers.
