parseArriba

parseArriba takes the identified fusion transcript results from Arriba and saves as a GVF file. The GVF file can be later used to call variant peptides using callVariant.

Reference Version

The version of reference genome and proteome FASTA and annotation GTF MUST be consistent across all analysis.

Usage

usage: moPepGen parseArriba [-h] -i <file> -o <file>
                            [--min-split-read1 <value>]
                            [--min-split-read2 <value>]
                            [--min-confidence <choice>] --source SOURCE
                            [-g <file>] [-a <file>]
                            [--reference-source {GENCODE,ENSEMBL}]
                            [--index-dir [<file>]]
                            [--debug-level <value|number>] [-q]

Parse the Arriba result to GVF format of variant records for moPepGen to call
variant peptides.

optional arguments:
  -h, --help            show this help message and exit
  -i <file>, --input-path <file>
                        File path to Arriba's output TSV file. Valid formats:
                        ['.tsv', '.txt'] (default: None)
  -o <file>, --output-path <file>
                        File path to the output file. Valid formats: ['.gvf']
                        (default: None)
  --min-split-read1 <value>
                        Minimal split_read1 value. (default: 1)
  --min-split-read2 <value>
                        Minimal split_read2 value. (default: 1)
  --min-confidence <choice>
                        Minimal confidence value. (default: medium)
  --source SOURCE       Variant source (e.g. gSNP, sSNV, Fusion) (default:
                        None)
  --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)
  --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)

Arguments

-h, --help

show this help message and exit

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

File path to Arriba's output TSV file. Valid formats: ['.tsv', '.txt']

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

File path to the output file. Valid formats: ['.gvf']

--min-split-read1 <value> int

Minimal split_read1 value. int
Default: 1

--min-split-read2 <value> int

Minimal split_read2 value. int
Default: 1

--min-confidence <choice> str

Minimal confidence value. str
Default: medium
Choices: dict_keys(['low', 'medium', 'high'])

--source str

Variant source (e.g. gSNP, sSNV, Fusion)

-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']

--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.

--debug-level <value|number> str

Debug level. str
Default: INFO

-q, --quiet

Quiet
Default: False