translate-structs

Translate transcript structures to primary structures.

Usage

Template:

exacto translate-structs \
    --transcript-structures-tsv-file <transcript_structures_tsv_file> \
    --rna-variant-calls-tsv-file <rna_variant_calls_tsv_file> \
    --integrated-variants-tsv-file <integrated_variants_tsv_file> \
    --strategy <longest_orf|all_orfs> \
    --output-tsv-file <output_tsv_file> \
    --output-fasta-file <output_fasta_file> \
    [--num-threads NUM_THREADS]

Example:

exacto translate-structs \
    --transcript-structures-tsv-file rna_variants_outputs/tumor_exacto_transcript_structures.tsv \
    --rna-variant-calls-tsv-file rna_variants_outputs/tumor_exacto_rna_variant_calls.tsv \
    --integrated-variants-tsv-file tumor_dna_rna_variants_integrated.tsv \
    --strategy longest_orf \
    --output-tsv-file tumor_primary_structures.tsv \
    --output-fasta-file tumor_primary_structures.fasta

Description

Translate transcript structures to primary structures.

At a glance

Inputs: *.tsv (transcript structures), *.tsv (RNA variants), *.tsv (integrated variants)

Outputs: *.tsv (primary structures), *.fasta (primary structures FASTA)

Typical next step: call-peptide-vars

Required arguments

Flag	Type	Description
`--transcript-structures-tsv-file`	`str`	Input transcript structures TSV file.
`--rna-variant-calls-tsv-file`	`str`	Input RNA variant calls TSV file.
`--integrated-variants-tsv-file`	`str`	Input integrated variants TSV file.
`--strategy`	`str` (longest_orf\|all_orfs)	Translation strategy.
`--output-tsv-file`	`str`	Output TSV file.
`--output-fasta-file`	`str`	Output FASTA file.

Optional arguments

Flag	Type	Default	Description
`--num-threads`	`int`	`4`	Number of threads.