callAltTranslation

Usage

usage: moPepGen callAltTranslation [-h] -o <file> [--w2f-reassignment]
                                   [--selenocysteine-termination] [-g <file>]
                                   [-a <file>]
                                   [--reference-source {GENCODE,ENSEMBL}]
                                   [-p <file>]
                                   [--invalid-protein-as-noncoding]
                                   [--index-dir [<file>]] [-c <value>]
                                   [--cleavage-exception <value>]
                                   [-m <number>] [-w <number>] [-l <number>]
                                   [-x <number>]
                                   [--debug-level <value|number>] [-q]

optional arguments:
  -h, --help            show this help message and exit
  -o <file>, --output-path <file>
                        Output path to the alternative translation peptide
                        FASTA. Valid formats: ['.fa', '.fasta'] (default:
                        None)
  --w2f-reassignment    Include peptides with W > F (Tryptophan to
                        Phenylalanine) reassignment. (default: False)
  --selenocysteine-termination
                        Include peptides of selenoprotiens that the UGA is
                        treated as termination instead of Sec. (default:
                        False)
  --debug-level <value|number>
                        Debug level. (default: INFO)
  -q, --quiet           Quiet (default: False)

Reference Files:
  -g <file>, --genome-fasta <file>
                        Path to the genome assembly FASTA file. Only ENSEMBL
                        and GENCODE are supported. Its version must be the
                        same as the annotation GTF and proteome FASTA
                        (default: None)
  -a <file>, --annotation-gtf <file>
                        Path to the annotation GTF file. Only ENSEMBL and
                        GENCODE are supported. Its version must be the same as
                        the genome and proteome FASTA. (default: None)
  --reference-source {GENCODE,ENSEMBL}
                        Source of reference genome and annotation. (default:
                        None)
  -p <file>, --proteome-fasta <file>
                        Path to the translated protein sequence FASTA file.
                        Only ENSEMBL and GENCODE are supported. Its version
                        must be the same as genome FASTA and annotation GTF.
                        (default: None)
  --invalid-protein-as-noncoding
                        Treat any transcript that the protein sequence is
                        invalid ( contains the * symbol) as noncoding.
                        (default: False)
  --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)

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

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

Output path to the alternative translation peptide FASTA. Valid formats: ['.fa', '.fasta']

--w2f-reassignment

Include peptides with W > F (Tryptophan to Phenylalanine) reassignment.
Default: False

--selenocysteine-termination

Include peptides of selenoprotiens that the UGA is treated as termination instead of Sec.
Default: False

-g, --genome-fasta <file> Path

Path to the genome assembly FASTA file. Only ENSEMBL and GENCODE are supported. Its version must be the same as the annotation GTF and proteome FASTA

-a, --annotation-gtf <file> Path

Path to the annotation GTF file. Only ENSEMBL and GENCODE are supported. Its version must be the same as the genome and proteome FASTA.

--reference-source str

Source of reference genome and annotation.
Choices: ['GENCODE', 'ENSEMBL']

-p, --proteome-fasta <file> Path

Path to the translated protein sequence FASTA file. Only ENSEMBL and GENCODE are supported. Its version must be the same as genome FASTA and annotation GTF.

--invalid-protein-as-noncoding

Treat any transcript that the protein sequence is invalid ( contains the * symbol) as noncoding.
Default: False

--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.

-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

Alternative translation

Alternative translation is when a different peptide is generated from the same transcript without any changes in the nucleotide sequence of the transcript.

Selenocysteine Termination

In eukaryotes, the UGA on some mRNAs can be decoded into selenocysteine instead of being recognized as a stop codon, and these proteins are called selenoproteins. However, the decoding of UGA is regulated by complex signals including mRNA and sec-tRNA abundance, which could result in two proteoforms: one with UGA read through and one with termination at the stop codon. Selenocysteine termination is used to represent the later situation. Selenocysteine terminations are not written into any GVF files but are represented in the format of SECT-<pos> where pos is the position of the selenocysteine UGA being recognized as a stop codon in the gene.

Tryptophan > Phenylalanine Codon Reassignment

Tryptophan > Phenylalanine substitutants, described in [Patasker, et al., happen when cellular tryptophan is depleted and phenylalanine is reassigned to tryptophan codons to continue protein synthesis. The process largely exists in tumor cells. Similar to selenocysteine termination, W > F substitutants are not written in GVFs, but are represented in the format of W2F-<pos>. Noted that the pos is a peptide coordinate (i.e., zeroed at the beginning of the peptide).