call-peptide-vars

Call peptide variants from primary structures.

Usage

Template:

exacto call-peptide-vars \
    --primary-structures-tsv-file <primary_structures_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 \
    --primary-structures-tsv-file tumor_primary_structures.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 primary structures.

At a glance

Inputs: *.tsv (primary structures), *.fasta (reference proteome)

Outputs: *.tsv (peptide variants), *.fasta (peptide sequences)

Typical next step: Endpoint — final mutant peptide output

Required arguments

Flag	Type	Description
`--primary-structures-tsv-file`	`str`	Input primary structures TSV file.
`--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.