parseREDItools

parseREDItools takes RNA editing results called by REDItools and saves them as a GVF file. The GVF file can then be 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 parseREDItools [-h] -i <file> -o <file>
                               [--transcript-id-column <number>]
                               [--min-coverage-alt <number>]
                               [--min-frequency-alt <value>]
                               [--min-coverage-rna <value>]
                               [--min-coverage-dna <number>] --source SOURCE
                               [-a <file>]
                               [--reference-source {GENCODE,ENSEMBL}]
                               [--index-dir [<file>]]
                               [--debug-level <value|number>] [-q]

Parse the REDItools result to a GVF format of variant records for moPepGen to
call variant peptides. The genome

optional arguments:
  -h, --help            show this help message and exit
  -i <file>, --input-path <file>
                        File path to REDItools' TSV output. Valid formats:
                        ['.tsv', '.txt'] (default: None)
  -o <file>, --output-path <file>
                        File path to the output file. Valid formats: ['.gvf']
                        (default: None)
  --transcript-id-column <number>
                        The column index for transcript ID. If your REDItools
                        table does not contains it, use the AnnotateTable.py
                        from the REDItools package. (default: 17)
  --min-coverage-alt <number>
                        Minimal read coverage of alterations to be parsed.
                        (default: 3)
  --min-frequency-alt <value>
                        Minimal frequency of alteration to be parsed.
                        (default: 0.1)
  --min-coverage-rna <value>
                        Minimal read coverage at the alteration site of RNAseq
                        data of reference and all alterations. (default: 10)
  --min-coverage-dna <number>
                        Minimal read coverage at the alteration site of WGS.
                        Set it to -1 to skip checking this. (default: 10)
  --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:
  -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 REDItools' TSV output. Valid formats: ['.tsv', '.txt']

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

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

--transcript-id-column <number> int

The column index for transcript ID. If your REDItools table does not contains it, use the AnnotateTable.py from the REDItools package. int
Default: 17

--min-coverage-alt <number> int

Minimal read coverage of alterations to be parsed. int
Default: 3

--min-frequency-alt <value> float

Minimal frequency of alteration to be parsed. float
Default: 0.1

--min-coverage-rna <value> int

Minimal read coverage at the alteration site of RNAseq data of reference and all alterations. int
Default: 10

--min-coverage-dna <number> int

Minimal read coverage at the alteration site of WGS. Set it to -1 to skip checking this. int
Default: 10

--source str

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

-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