translate-seqs

Translate transcript sequences in a long-read RNA-seq FASTX file or RNA sequence to peptide sequences.

Usage

Template:

exacto translate-seqs \
    --strategy <longest_orf|all_orfs> \
    [--fastx-file FASTX_FILE] \
    [--sequence SEQUENCE] \
    [--start-codons START_CODONS [START_CODONS ...]] \
    [--output-tsv-file OUTPUT_TSV_FILE] \
    [--output-fasta-file OUTPUT_FASTA_FILE] \
    [--num-threads NUM_THREADS]

Example:

exacto translate-seqs \
    --fastx-file transcripts.fasta \
    --strategy longest_orf \
    --output-tsv-file translations.tsv \
    --output-fasta-file translations.fasta

Description

Translate transcript sequences in a long-read RNA-seq FASTX file or RNA sequence to peptide sequences.

At a glance

Inputs: *.fasta, *.fastq, or a raw sequence string

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

Typical next step: Standalone utility — not part of the main proteoform pipeline

Required arguments

Flag	Type	Description
`--fastx-file`	`str`	Input FASTA or FASTQ file.
`--sequence`	`str`	Directly input a transcript sequence.
`--strategy`	`str` (longest_orf\|all_orfs)	Translation strategy.

Optional arguments

Flag	Type	Default	Description
`--start-codons`	`str`	`AUG`	One or more start codons. Pass multiple as: –start-codons AUG GUG CUG.
`--output-tsv-file`	`str`		Output TSV file.
`--output-fasta-file`	`str`		Output FASTA file.
`--num-threads`	`int`	`4`	Number of threads.