helixforge viz

Render per-locus plots, interactive pages, or browser tracks for a run.

Visualizes a reconciled run. Because the rich ReconciledGene set is not serialised to disk, viz takes the same inputs as reconcile and rebuilds the gene set via the pipeline before plotting, so it needs the full pipeline option set, not a finished GFF3.

Output (written under --out-dir), by --mode:

static: one figure per locus (--fmt svg/pdf/png); --top-n keeps the N most AS-complex loci, --gene restricts to a single gene id
interactive: an HTML index of interactive per-locus pages
tracks: a BED12 browser track (.bed)

Options

Option	Description
`--genome`	Genome FASTA (required). (required)
`--helixer`	Helixer GFF3 (required). (required)
`--helixer-h5`	Helixer confidence HDF5: a combined file, the '_input.h5' metadata half, or the '_predictions.h5' softmax half (the partner half is auto-detected as the sibling, or named via --helixer-input-h5).
`--helixer-input-h5`	Helixer '_input.h5' metadata half (coordinate mapping). Needed only when --helixer-h5 is a bare '_predictions.h5' whose '*_input.h5' sibling is not co-located. Mirrors 'confidence --input-h5'.
`--stringtie`	StringTie GTF, one per sample. Comma-separated or repeated. (repeatable)
`--stringtie-list`	File of StringTie GTF paths, one per line (blank lines and # comments ignored).
`--bam`	RNA-seq BAM. Comma-separated or repeated. (repeatable)
`--bam-list`	File of BAM paths, one per line (blank lines and # comments ignored).
`--bigwig`	Coverage bigWig. Comma-separated or repeated. (repeatable)
`--bigwig-list`	File of bigWig paths, one per line (blank lines and # comments ignored).
`--star-sj`	STAR SJ.out.tab. Comma-separated or repeated. (repeatable)
`--star-sj-list`	File of SJ.out.tab paths, one per line (blank lines and # comments ignored).
`--miniprot`	miniprot GFF for backstop CDS projection. Not a substitute for --protein-db; does not enable Mikado.
`--protein-db`	Protein FASTA for DIAMOND homology. Required (with StringTie) to enable Mikado reconciliation and isoform discovery.
`--te-annotation`	EDTA TE GFF3. Flags TE-overlapping models (TE_OVERLAP) and reclassifies good-ORF genes above --te-overlap-threshold as transposable_element. Uses the EDTA Classification order; knob/satellite/low-complexity never gate.
`--te-overlap-threshold`	Model-fraction TE overlap at/above which a good-ORF gene is reclassified transposable_element (default 0.5). (default: `0.5`)
`--te-class`	EDTA Classification order to treat as a TE (repeatable). Default covers true TE orders (LTR, DNA, MITE, TIR, Helitron, LINE, SINE) and excludes knob/satellite/low-complexity. (repeatable)
`--transdecoder-bin-dir`
`--backstop-transdecoder`, `--no-backstop-transdecoder`	(default: `False`)
`--portcullis-bin`
`--mikado-bin`	(default: `mikado`)
`--diamond-bin`	(default: `diamond`)
`--mikado-configure`, `--no-mikado-configure`	(default: `True`)
`--functional-annotation`, `--no-functional-annotation`	Run the opt-in functional-annotation hook (InterProScan / eggNOG). (default: `False`)
`--functional-tool`	Annotation tool(s) to run for --functional-annotation. (choices: interproscan/eggnog/both; default: `interproscan`)
`--functional-db`	eggNOG data dir (required for --functional-tool eggnog/both).
`--interproscan-bin`	InterProScan binary (bare command or absolute path). (default: `interproscan.sh`)
`--eggnog-bin`	eggNOG-mapper binary (bare command or absolute path). (default: `emapper.py`)
`--transl-table`	NCBI genetic-code table id for CDS validation (default 1 = standard nuclear code). (default: `1`)
`--transl-table-map`	Per-seqid genetic-code overrides; lines 'seqid=table' (e.g. chrMt=1, chrPt=11). 'seqid<TAB/space>table' also accepted. Overrides --transl-table for the named seqids.
`--scoring-profile`	(choices: strict/permissive; default: `strict`)
`--helixer-reference`, `--no-helixer-reference`	Inject Helixer as is_reference=true. (default: `True`)
`--helixer-support-weight`	Scale external helixer_support (0 disables coupling). (default: `1.0`)
`--output-prefix`	(default: `helixforge`)
`--report-path`
`--id-map-path`
`--work-dir`
`--region`	seqid or seqid:start-end.
`--chunk-id`
`--id-base`	Lowest HFG number for this chunk's reserved range. (default: `1`)
`--novel-base`	Lowest HFG number for this chunk's novel sub-range. (default: `90000`)
`--procs`	(default: `1`)
`--threads`	(default: `4`)
`--min-tpm`	(default: `0.5`)
`--min-samples`	(default: `1`)
`--coverage-threshold`	(default: `2.0`)
`--near-zero-coverage`	(default: `0.1`)
`--as-report`, `--no-as-report`	(default: `True`)
`--only-confirmed-introns`, `--allow-unconfirmed-introns`	(default: `True`)
`--max-isoforms`	(default: `5`)
`--keep-retained-introns`, `--drop-retained-introns`	(default: `False`)
`--pad`, `--no-pad`	Unify isoform termini (the strongest consistency lever). (default: `True`)
`--chimera-split`, `--no-chimera-split`	(default: `True`)
`--flank`	(default: `200`)
`--reciprocal-overlap`	(default: `0.5`)
`--min-cds-overlap`	(default: `0.6`)
`--min-cdna-overlap`	(default: `0.6`)
`--admit-novel`, `--no-admit-novel`	(default: `False`)
`--novel-evidence-floor`
`--trace-primary`, `--no-trace-primary`	Elect the canonical/primary isoform per gene by ranked-choice voting (TRaCE) instead of highest combined_score. (default: `False`)
`--trace-max-aed`	TRaCE: max AED for a sample to vote for a candidate. (default: `0.5`)
`--trace-min-tpm`	TRaCE: min TPM for a sample's assembled transcript to vote. (default: `0.5`)
`--trace-min-overlap`	TRaCE: min proportion-overlap for a sample transcript to vote. (default: `0.5`)
`--trace-weight-domain`	TRaCE: domain-coverage voter weight. (default: `9.0`)
`--trace-weight-protein`	TRaCE: protein (CDS) length voter weight. (default: `6.0`)
`--trace-weight-cdna`	TRaCE: transcript (cDNA) length voter weight. (default: `3.0`)
`--trace-use-domain`, `--no-trace-use-domain`	TRaCE: include the domain-coverage voter when per-isoform domain coverage is available. (default: `True`)
`--short-cds-threshold`	(default: `300`)
`--short-exon-threshold`	(default: `10`)
`--long-intron-threshold`	(default: `100000`)
`--junction-tolerance`	(default: `0`)
`--junction-min-reads`	(default: `3`)
`--out-dir`	Directory for the figures / tracks. (required)
`--mode`	Output kind. (choices: static/interactive/tracks; default: `static`)
`--gene`	Restrict to a single gene id.
`--top-n`	Static mode: only the N most AS-complex loci.
`--fmt`	Static figure format (svg/pdf/png). (default: `svg`)

Examples

  # static SVG of the 50 most AS-complex loci
  helixforge viz --genome genome.fa --helixer helixer.gff3 \
      --helixer-h5 helixer.h5 --stringtie-list stringtie.list \
      --out-dir figures --mode static --top-n 50

  # one gene, as a PDF
  helixforge viz --genome genome.fa --helixer helixer.gff3 \
      --out-dir figures --mode static --gene HFG_00042 --fmt pdf

  # BED12 browser track for the whole run
  helixforge viz --genome genome.fa --helixer helixer.gff3 \
      --out-dir tracks --mode tracks