build-transcriptome-var-graph

Build a transcriptome variation graph: one sequence per transcript model of the call-rna-transcript-vars model alignments table, named by its assembled_transcript_name, in the order of the table. A model whose rows do not join into one path is logged and skipped.

Usage

Template:

exacto build-transcriptome-var-graph \
    --transcript-structures-tsv-file <transcript_structures_tsv_file> \
    --fasta-file <fasta_file> \
    --output-fasta-file <output_fasta_file> \
    [--graph-type GRAPH_TYPE] \
    [--num-threads NUM_THREADS] \
    [--batch-size BATCH_SIZE]

Example:

exacto build-transcriptome-var-graph \
    --transcript-structures-tsv-file rna_variants/tumor_exacto_assembled_transcript_model_alignments.tsv \
    --fasta-file reference_genome.fasta \
    --output-fasta-file tumor_transcriptome_var_graph.fasta

Description

Build a transcriptome variation graph: one sequence per transcript model of the call-rna-transcript-vars model alignments table, named by its assembled_transcript_name, in the order of the table. A model whose rows do not join into one path is logged and skipped.

NoteAt a glance

Inputs: *_exacto_assembled_transcript_model_alignments.tsv (from call-rna-transcript-vars), *.fasta (reference genome)

Outputs: *.fasta (transcriptome variation graph sequences, one record per assembled transcript)

Typical next step: Endpoint — feeds downstream graph-aware analyses

Required arguments

Flag	Type	Description
--transcript-structures-tsv-file	str	Transcript model alignments TSV file, the ’*_exacto_assembled_transcript_model_alignments.tsv’ of call-rna-transcript-vars. Required columns: ‘assembled_transcript_name’, ‘index’, ‘chromosome_1’, ‘position_1’, ‘operation_1’, ‘strand_1’, ‘chromosome_2’, ‘position_2’, ‘operation_2’, ‘strand_2’, ‘sequence’ (genome-forward). Optional: ‘num_cycles’; a model with a row that walks back (a duplication or back-splice) needs it and is skipped otherwise. Each output record is named by its ‘assembled_transcript_name’.
--fasta-file	str	Reference genome FASTA file (variation graph backbone).
--output-fasta-file	str	Output FASTA file.

Optional arguments

Flag	Type	Default	Description
--graph-type	str	individual	Variation graph type. Either ‘individual’ or ‘population’.
--num-threads	int	4	Number of threads.
--batch-size	int	1000	Batch size.