encodeFasta

This module takes in a variant peptide FASTA file and encodes the fasta headers with 36-digit long UUID (32 digits of hexdecimal characters and 4 hypens). The original headers together with the UUIDs arer saved into the dict file at the same location. This resolves the problems that some proteomic search engines have strick requirement on the FASTA header length.

Usage

usage: moPepGen encodeFasta [-h] -i <file> -o <file> [--decoy-string <value>]
                            [--decoy-string-position <value>]
                            [--debug-level <value|number>] [-q]

Encode variant peptide FASTA file header.

optional arguments:
  -h, --help            show this help message and exit
  -i <file>, --input-path <file>
                        Input FASTA file, must be generated by moPepGen
                        callVariant. Valid formats: ['.fa', '.fasta']
                        (default: None)
  -o <file>, --output-path <file>
                        File path to the output file. Valid formats: ['.fa',
                        '.fasta'] (default: None)
  --debug-level <value|number>
                        Debug level. (default: INFO)
  -q, --quiet           Quiet (default: False)

Decoy Database Parameters:
  --decoy-string <value>
                        The decoy string that is combined with the FASTA
                        header for decoy sequences. (default: DECOY_)
  --decoy-string-position <value>
                        Should the decoy string be placed at the start or end
                        of FASTA headers? (default: prefix)

Arguments

-h, --help

show this help message and exit

-i, --input-path <file> Path

Input FASTA file, must be generated by moPepGen callVariant. Valid formats: ['.fa', '.fasta']

-o, --output-path <file> Path

File path to the output file. Valid formats: ['.fa', '.fasta']

--decoy-string <value> str

The decoy string that is combined with the FASTA header for decoy sequences. str
Default: DECOY_

--decoy-string-position <value> str

Should the decoy string be placed at the start or end of FASTA headers? str
Default: prefix
Choices: ['prefix', 'suffix']

--debug-level <value|number> str

Debug level. str
Default: INFO

-q, --quiet

Quiet
Default: False