FAQ

FAQ

"index already exists" — what do I do?

This is informational, not an error. prot2exon fetch caches indexes under ~/.cache/prot2exon/; on the second invocation it just prints using cached index: /path/to/yeast.idx (--force to rebuild) and prints the path. Pass --force if you actually want to rebuild from the upstream GTF.

My TSV row has cds_length_mismatch = true — bug?

Usually not. It flags cases where the sum of CDS lengths isn't a clean multiple of 3, which happens legitimately for:

• Selenoproteins (Sec) — UGA stop codon read through as selenocysteine.
• Programmed readthrough / stop-codon recoding.
• Incomplete CDS — transcripts annotated as cds_start_NF, cds_end_NF, or mRNA_end_NF.

cds_nt_remainder (1 or 2) tells you which side. The mapping is still emitted; you just lose codon-precision at the affected end.

A query has reason = no_CDS_for_protein — what's going on?

You probably passed a transcript ID for a non-coding transcript (lncRNA, processed transcript, …). There's no CDS to map onto, so the row goes to unmapped_domains.tsv. The summary's input_id_type column distinguishes ENSP / ENST queries.

How do I build a query BED from a domain database (Pfam, InterProScan, UniProt)?

Use the prot2exon.prepare helpers — from_pfam(), from_interproscan(), from_uniprot_features() — which turn those tools' standard outputs into a DataFrame that Mapper.map_batch() consumes directly (the parsing/ CLI wrappers do the same from the command line). See the Python API page for the exact signatures.

How does prot2exon handle codons split across an exon boundary?

Codons that straddle two CDS exons (1+2 or 2+1 patterns) are handled correctly — the mapper tracks cds_nt_start / cds_nt_end across the exon boundary so aa coordinates round-trip cleanly. CDS exons are split only when the domain partially covers them, never on the codon boundary.

MANE Select and Ensembl canonical — where are they?

is_mane_select and is_ensembl_canonical columns are present on every TSV. They're booleans (true / false) parsed from GENCODE/Ensembl tag annotations. RefSeq GTFs don't carry MANE Select tags, so both columns are NA there.

The plot looks empty / I see no UTRs

Two common causes:

• You loaded domain_cds_segments.tsv instead of isoform_structure.tsv. The CDS table doesn't include UTR rows by design — only the full isoform table does.
• You passed --no-utr to the plotter, or unchecked Show UTRs in the interactive viewer.

The viewer shows long stretches of empty intron — fix?

Use compact mode. CLI: --compact-genomic (matplotlib) or the Compact (introns = 80 bp) radio in the interactive viewer. Long human genes (TP53 spans ~19 kb) become legible at exon resolution.

My --html plotly file is huge

That's expected — plotly bundles its full JS engine in every standalone HTML (~3 MB). If size matters, use --html-interactive instead — the interactive viewer is ~35 KB and has no JS dependency.

Can I run prot2exon on Windows?

The Python wrapper works on Windows. The C++ binary should build cleanly under MSVC 2019+ or MinGW, but is mainly tested on Linux. WSL is the path of least friction.

How do I cite prot2exon?

A formal citation will land when the accompanying manuscript is posted. Until then, please cite the repository URL.

Where do I report a bug?

Open an issue on the GitHub repo. A minimal reproducer (the GTF lines or BED row that triggers it, plus the exact CLI you ran) makes triage 10× faster.

I want to contribute — where do I start?

• Bug fixes — open a PR with a regression test under software_tests/ (pytest; pick the module that fits — test_correctness.py for mapping output, test_compat.py for GTF dialects, etc.).
• New plot styles — both matplotlib (plot.py) and the JS viewer (_interactive_html.py) are templated; copy an existing draw function and add a CLI flag.
• New input adapters — parsing/prepare_from_*.py is the conventional spot for "turn external format X into prot2exon BED".
• New genome onboarding presets — extend _resolve_url in python/prot2exon/fetch.py.