call-peptide-vars

Call peptide variants from proteoforms.

Usage

Template:

exacto call-peptide-vars \
    --proteoforms-tsv-file <proteoforms_tsv_file> \
    --reference-fasta-file <reference_fasta_file> \
    --output-tsv-file <output_tsv_file> \
    --output-fasta-file <output_fasta_file> \
    [--min-k MIN_K] \
    [--max-k MAX_K] \
    [--num-threads NUM_THREADS]

Example:

exacto call-peptide-vars \
    --proteoforms-tsv-file translation/tumor_exacto_proteoforms.tsv \
    --reference-fasta-file reference_proteome.fasta \
    --output-tsv-file tumor_peptide_variants.tsv \
    --output-fasta-file tumor_peptide_variants.fasta

Description

Call peptide variants from proteoforms.

At a glance

Inputs: *_exacto_proteoforms.tsv (from translate-transcripts), *.fasta (reference proteome)

Outputs: *.tsv (mutant peptides), *.fasta (mutant peptide sequences)

Typical next step: Endpoint — final mutant peptide output

Required arguments

Flag	Type	Description
`--proteoforms-tsv-file`	`str`	Input proteoforms TSV file (output from exacto translate-transcripts).
`--reference-fasta-file`	`str`	Reference proteome FASTA file.
`--output-tsv-file`	`str`	Output TSV file.
`--output-fasta-file`	`str`	Output FASTA file.

Optional arguments

Flag	Type	Default	Description
`--min-k`	`int`	`8`	Minimum peptide length.
`--max-k`	`int`	`11`	Maximum peptide length.
`--num-threads`	`int`	`4`	Number of threads.