updateIndex

updateIndex creates new canoincal peptide pool to a moPepGen index dir created by generateIndex. This command is useful when you want to use a different enzyme or cleavage settings (e.g., miscleavages, min_length) with the same reference genome, annotation, and proteome.

Usage

usage: moPepGen updateIndex [-h] [--index-dir [<file>]] [-f] [-c <value>]
                            [--cleavage-exception <value>] [-m <number>]
                            [-w <number>] [-l <number>] [-x <number>]
                            [--debug-level <value|number>] [-q]

Update moPepGen index

optional arguments:
  -h, --help            show this help message and exit
  --index-dir [<file>]  Path to the directory of index files generated by
                        moPepGen generateIndex. If given, --genome-fasta,
                        --proteome-fasta and --anntotation-gtf will be
                        ignored. (default: None)
  -f, --force           Force write data to index dir. (default: False)
  --debug-level <value|number>
                        Debug level. (default: INFO)
  -q, --quiet           Quiet (default: False)

Cleavage Parameters:
  -c <value>, --cleavage-rule <value>
                        Enzymatic cleavage rule. (default: trypsin)
  --cleavage-exception <value>
                        Enzymatic cleavage exception. (default: auto)
  -m <number>, --miscleavage <number>
                        Number of cleavages to allow per non-canonical
                        peptide. (default: 2)
  -w <number>, --min-mw <number>
                        The minimal molecular weight of the non-canonical
                        peptides. (default: 500.0)
  -l <number>, --min-length <number>
                        The minimal length of non-canonical peptides,
                        inclusive. (default: 7)
  -x <number>, --max-length <number>
                        The maximum length of non-canonical peptides,
                        inclusive. (default: 25)

Arguments

-h, --help

show this help message and exit

--index-dir <file> Path

Path to the directory of index files generated by moPepGen generateIndex. If given, --genome-fasta, --proteome-fasta and --anntotation-gtf will be ignored.

-f, --force

Force write data to index dir.
Default: False

-c, --cleavage-rule <value> str

Enzymatic cleavage rule. str
Default: trypsin
Choices: ['arg-c', 'asp-n', 'bnps-skatole', 'caspase 1', 'caspase 2', 'caspase 3', 'caspase 4', 'caspase 5', 'caspase 6', 'caspase 7', 'caspase 8', 'caspase 9', 'caspase 10', 'chymotrypsin high specificity', 'chymotrypsin low specificity', 'clostripain', 'cnbr', 'enterokinase', 'factor xa', 'formic acid', 'glutamyl endopeptidase', 'granzyme b', 'hydroxylamine', 'iodosobenzoic acid', 'lysc', 'lysn', 'ntcb', 'pepsin ph1.3', 'pepsin ph2.0', 'proline endopeptidase', 'proteinase k', 'staphylococcal peptidase i', 'thermolysin', 'thrombin', 'trypsin', 'trypsin_exception']

--cleavage-exception <value> str

Enzymatic cleavage exception. str
Default: auto

-m, --miscleavage <number> int

Number of cleavages to allow per non-canonical peptide. int
Default: 2

-w, --min-mw <number> float

The minimal molecular weight of the non-canonical peptides. float
Default: 500.0

-l, --min-length <number> int

The minimal length of non-canonical peptides, inclusive. int
Default: 7

-x, --max-length <number> int

The maximum length of non-canonical peptides, inclusive. int
Default: 25

--debug-level <value|number> str

Debug level. str
Default: INFO

-q, --quiet

Quiet
Default: False