translate-seqs

Translate transcript sequences in a long-read RNA-seq FASTA or FASTQ file to peptide sequences.

Usage

Template:

exacto translate-seqs \
    --strategy <longest_orf|all_orfs> \
    [--fastq-file FASTQ_FILE] \
    [--fasta-file FASTA_FILE] \
    [--sequence SEQUENCE] \
    [--output-tsv-file OUTPUT_TSV_FILE] \
    [--output-fasta-file OUTPUT_FASTA_FILE] \
    [--num-threads NUM_THREADS] \
    [--temp-dir TEMP_DIR] \
    [--gzip GZIP]

Example:

exacto translate-seqs \
    --fasta-file tumor_transcriptome_assembly.fasta \
    --strategy longest_orf \
    --output-tsv-file tumor_translations.tsv \
    --output-fasta-file tumor_translations.fasta

Description

Translate transcript sequences in a long-read RNA-seq FASTA or FASTQ file 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
`--fastq-file`	`str`	Input FASTQ or FASTQ.GZ file.
`--fasta-file`	`str`	Input FASTA or FASTA.GZ file.
`--sequence`	`str`	Directly input a transcript sequence.
`--strategy`	`str` (longest_orf\|all_orfs)	Translation strategy.

Optional arguments

Flag	Type	Default	Description
`--output-tsv-file`	`str`		Output TSV file.
`--output-fasta-file`	`str`		Output FASTA file.
`--num-threads`	`int`	`4`	Number of threads.
`--temp-dir`	`str`		Temp directory.
`--gzip`	`str2bool`	`yes`	If ‘yes’, gzip the output TSV and FASTA file.