translate-transcripts

Translate transcripts to proteoforms.

Usage

Template:

exacto translate-transcripts \
    --assembled-transcript-model-alignments-tsv-file <assembled_transcript_model_alignments_tsv_file> \
    --assembled-transcript-variants-tsv-file <assembled_transcript_variants_tsv_file> \
    --dna-variants-tsv-file <dna_variants_tsv_file> \
    --integrated-variants-tsv-file <integrated_variants_tsv_file> \
    --strategy <longest_orf|all_orfs> \
    --output-dir <output_dir> \
    [--output-prefix OUTPUT_PREFIX] \
    [--rna-consensus-tsv-file RNA_CONSENSUS_TSV_FILE] \
    [--assembled-transcripts-support-tsv-file ASSEMBLED_TRANSCRIPTS_SUPPORT_TSV_FILE] \
    [--stitched-transcripts-tsv-file STITCHED_TRANSCRIPTS_TSV_FILE] \
    [--start-codons START_CODONS [START_CODONS ...]] \
    [--num-threads NUM_THREADS]

Example:

exacto translate-transcripts \
    --assembled-transcript-model-alignments-tsv-file rna_variants/tumor_exacto_assembled_transcript_model_alignments.tsv \
    --assembled-transcript-variants-tsv-file rna_variants/tumor_exacto_assembled_transcript_variants.tsv \
    --dna-variants-tsv-file tumor_somatic_dna_variants.tsv \
    --integrated-variants-tsv-file tumor_integrated_variants.tsv \
    --rna-consensus-tsv-file pass2/tumor_pass2_exacto_rna_consensus.tsv \
    --stitched-transcripts-tsv-file stitched/tumor_exacto_stitched_transcripts.tsv \
    --strategy longest_orf \
    --output-dir translation/ \
    --output-prefix tumor

Description

Translate transcripts to proteoforms.

At a glance

Inputs: *_exacto_rna_consensus.tsv (from determine-rna-consensus) or an assembled transcript support TSV, optionally *_exacto_stitched_transcripts.tsv, the call-rna-transcript-vars model alignments and variants TSVs, *.tsv (DNA variants), *.tsv (integrated variants)

Outputs: {prefix}_exacto_proteoforms.tsv, {prefix}_exacto_proteoforms.fasta, {prefix}_exacto_proteoform_nucleotides.tsv

Typical next step: call-peptide-vars

Required arguments

Flag	Type	Description
`--assembled-transcript-model-alignments-tsv-file`	`str`	Input assembled transcript model alignments TSV file (output from exacto call-rna-transcript-vars).
`--assembled-transcript-variants-tsv-file`	`str`	Input assembled transcript variants TSV file (output from exacto call-rna-transcript-vars).
`--dna-variants-tsv-file`	`str`	Input DNA variants TSV file (output from exacto call-somatic-dna-vars).
`--integrated-variants-tsv-file`	`str`	Input integrated variants TSV file (output from exacto integrate-vars).
`--strategy`	`str` (longest_orf\|all_orfs)	Translation strategy.
`--output-dir`	`str`	Output directory.
`--output-prefix`	`str`	Output prefix.

Transcript sequence arguments (exactly one required)

Flag	Type	Default	Description
`--rna-consensus-tsv-file`	`str`		Input RNA consensus TSV file (output from exacto determine-rna-consensus; columns: cluster_id, consensus_sequence, num_reads, read_names). Transcripts are named by cluster ID, matching the FASTA that command writes.
`--assembled-transcripts-support-tsv-file`	`str`		Input RNA assembly support TSV file for transcripts assembled outside exacto (columns: assembled_transcript_name, sequence, read_names).

Optional arguments

Flag	Type	Default	Description
`--stitched-transcripts-tsv-file`	`str`		Input stitched transcripts TSV file written by exacto stitch-reference-transcripts (optional). Its stitched sequences replace the transcript sequences, joined by transcript name, so the call-rna-transcript-vars TSV files must come from the realigned stitched FASTA of the same stitch run. Adds reference-stitched provenance columns to both outputs: is_reference_stitched per nucleotide, and reference_stitched_amino_acid_intervals plus num_reference_stitched_amino_acids per proteoform.
`--start-codons`	`str`	`AUG`	One or more start codons. Pass multiple as: –start-codons AUG GUG CUG.
`--num-threads`	`int`	`4`	Number of threads.