callVariant
callVariant is the core of moPepGen. It takes multiple GVF files, generated
by any moPepGen parser, and calls variant peptides caused by genomic variants
using a graph-based algorithm. For any transcript, it creates a three-frame
transcript variant graph by incorporating all variants from any sources (SNV,
INDEL, fusion, alternative splicing, RNA editing, and circRNA). The transcript
variant graph is then translated into a peptide variant graph, followed by
converting to a cleavage graph based on the enzymatic cleavage rule. The
variant peptide graph is than used to call for variant peptides that contains
at least one variant, and do not present in the canonical peptide pool.
Usage
usage: moPepGen callVariant [-h] -i ['<files>'] [['<files>'] ...] -o <file>
[--graph-output-dir <file>]
[--max-adjacent-as-mnv MAX_ADJACENT_AS_MNV]
[--selenocysteine-termination]
[--w2f-reassignment] [--backsplicing-only]
[--coding-novel-orf]
[--max-variants-per-node <number> [<number> ...]]
[--additional-variants-per-misc <number> [<number> ...]]
[--min-nodes-to-collapse <number>]
[--naa-to-collapse <number>]
[--noncanonical-transcripts]
[--timeout-seconds TIMEOUT_SECONDS]
[--threads <number>] [-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]
Genomic variant data must be generated by one of the moPepGen parser. See
moPepGen --help
optional arguments:
-h, --help show this help message and exit
-i ['<files>'] [['<files>'] ...], --input-path ['<files>'] [['<files>'] ...]
File path to GVF files. Must be generated by any of
the moPepGen parsers. Can take multiple files. Valid
formats: ['.gvf'] (default: None)
-o <file>, --output-path <file>
File path to the output file. Valid formats:
['.fasta', '.fa'] (default: None)
--graph-output-dir <file>
Directory path that graph data are saved to. Graph
data are not saved if this is not given. (default:
None)
--max-adjacent-as-mnv MAX_ADJACENT_AS_MNV
Max number of adjacent variants that should be merged.
(default: 2)
--selenocysteine-termination
Include peptides of selenoprotiens that the UGA is
treated as termination instead of Sec. (default:
False)
--w2f-reassignment Include peptides with W > F (Tryptophan to
Phenylalanine) reassignment. (default: False)
--backsplicing-only For circRNA, only keep noncanonical peptides spaning
the backsplicing site. (default: False)
--coding-novel-orf Find alternative start site for coding transcripts.
(default: False)
--max-variants-per-node <number> [<number> ...]
Maximal number of variants per node. This argument can
be useful when there are local regions that are
heavily mutated. When creating the cleavage graph,
nodes containing variants larger than this value are
skipped. Setting to -1 will avoid checking for this.
(default: (7,))
--additional-variants-per-misc <number> [<number> ...]
Additional variants allowed for every miscleavage.
This argument is used together with --max-variants-
per-node to handle hypermutated regions. Setting to -1
will avoid checking for this. (default: (2,))
--min-nodes-to-collapse <number>
When making the cleavage graph, the minimal number of
nodes to trigger pop collapse. (default: 30)
--naa-to-collapse <number>
The number of bases used for pop collapse. (default:
5)
--noncanonical-transcripts
Process only noncanonical transcripts of fusion
transcripts and circRNA. Canonical transcripts are
skipped. (default: False)
--timeout-seconds TIMEOUT_SECONDS
Time out in seconds for each transcript. (default:
1800)
--threads <number> Set number of threads to be used. (default: 1)
--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
-i, --input-path ['<files>'] Path
File path to GVF files. Must be generated by any of the moPepGen parsers. Can take multiple files. Valid formats: ['.gvf']
-o, --output-path <file> Path
File path to the output file. Valid formats: ['.fasta', '.fa']
--graph-output-dir <file> Path
Directory path that graph data are saved to. Graph data are not saved if this is not given.
--max-adjacent-as-mnv int
Max number of adjacent variants that should be merged.
int
Default: 2
--selenocysteine-termination
Include peptides of selenoprotiens that the UGA is treated as termination instead of Sec.
Default: False
--w2f-reassignment
Include peptides with W > F (Tryptophan to Phenylalanine) reassignment.
Default: False
--backsplicing-only
For circRNA, only keep noncanonical peptides spaning the backsplicing site.
Default: False
--coding-novel-orf
Find alternative start site for coding transcripts.
Default: False
--max-variants-per-node <number> int
Maximal number of variants per node. This argument can be useful when there are local regions that are heavily mutated. When creating the cleavage graph, nodes containing variants larger than this value are skipped. Setting to -1 will avoid checking for this.
int
Default: (7,)
--additional-variants-per-misc <number> int
Additional variants allowed for every miscleavage. This argument is used together with --max-variants-per-node to handle hypermutated regions. Setting to -1 will avoid checking for this.
int
Default: (2,)
--min-nodes-to-collapse <number> int
When making the cleavage graph, the minimal number of nodes to trigger pop collapse.
int
Default: 30
--naa-to-collapse <number> int
The number of bases used for pop collapse.
int
Default: 5
--noncanonical-transcripts
Process only noncanonical transcripts of fusion transcripts and circRNA. Canonical transcripts are skipped.
Default: False
--timeout-seconds int
Time out in seconds for each transcript.
int
Default: 1800
--threads <number> int
Set number of threads to be used.
int
Default: 1
-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