From 3de75ad82564baf790c40fe897fd163310393e9c Mon Sep 17 00:00:00 2001 From: Alex Rubinsteyn Date: Tue, 29 Sep 2026 15:07:30 -0400 Subject: [PATCH 1/2] Import native Exacto sequence and transcript evidence --- CHANGELOG.md | 10 + docs/api.md | 10 + docs/combined-sources.md | 5 +- docs/exacto.md | 124 + docs/fragments.md | 8 +- mkdocs.yml | 1 + tests/data/exacto/LICENSE | 201 + tests/data/exacto/peptide-variants.tsv | 229 + tests/data/exacto/primary-structures.tsv | 7147 +++++++++++++++++ tests/data/exacto/provenance.json | 24 + tests/data/exacto/transcript-read-support.tsv | 2 + tests/data/exacto/translations.tsv.gz | Bin 0 -> 4511 bytes tests/test_consumer_workflows.py | 107 + tests/test_io_exacto.py | 262 + tests/test_twin_conformance.py | 26 + topiary/__init__.py | 7 +- topiary/io_exacto.py | 374 + 17 files changed, 8529 insertions(+), 8 deletions(-) create mode 100644 docs/exacto.md create mode 100644 tests/data/exacto/LICENSE create mode 100644 tests/data/exacto/peptide-variants.tsv create mode 100644 tests/data/exacto/primary-structures.tsv create mode 100644 tests/data/exacto/provenance.json create mode 100644 tests/data/exacto/transcript-read-support.tsv create mode 100644 tests/data/exacto/translations.tsv.gz create mode 100644 tests/test_io_exacto.py create mode 100644 topiary/io_exacto.py diff --git a/CHANGELOG.md b/CHANGELOG.md index 53bf369..8ab82c8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,16 @@ between published tags; older pre-5.0 notes are retained below. For current interfaces, see the [consumer guide](docs/consumer-guide.md). +## 5.88.0 + +- Import native Exacto peptide variants, primary structures and translations, + retaining original records, DNA/RNA links, alternative ORFs and unknown + specificity. Validate recovered sequence/novelty geometry against a pinned + public corpus; preserve transcript-scoped read membership when supplied (#365). +- Combine native observations with reported LENS/pVACseq candidates without + prediction, preserving evidence through CSV/TSV and explicit rescoring. + Add optional `read_exacto_fragments` for separate new-window scanning. + ## 5.87.0 - Link normalized events, nucleotide ORF hypotheses, full protein products and diff --git a/docs/api.md b/docs/api.md index 6aeb7fd..b4189f5 100644 --- a/docs/api.md +++ b/docs/api.md @@ -1,5 +1,15 @@ # API Reference +## Native Exacto input + +`read_exacto(path, *, sample_name, schema=None, primary_structures=None, +reference_name=None, tag=None, transcript_read_support=None, library_id=None, +read_set_id=None)` reads native sequence/evidence tables without prediction. +`read_exacto_fragments(path, **kwargs)` uses the same validation and returns +optional fragments for explicit new-window scanning. `EXACTO_SCHEMAS` and +`EXACTO_SCHEMA_COMMIT` describe the tested producer contract. See [Reading +Exacto](exacto.md) for supported files, evidence scope and composition examples. + ## Fragment identity and RNA outcomes A fragment record is identified by `(sample_name, fragment_id)`: the ID diff --git a/docs/combined-sources.md b/docs/combined-sources.md index c8bac92..053ba2f 100644 --- a/docs/combined-sources.md +++ b/docs/combined-sources.md @@ -28,9 +28,8 @@ ranked.to_csv("ranked-candidates.tsv", sep="\t", index=False) ``` Inputs may be `TopiaryResult` objects or normalized DataFrames. Existing readers -normalize LENS and pVACseq. Native Exacto parsing is separate work in -[#365](https://github.com/openvax/topiary/issues/365); an already normalized -ORF/RNA DataFrame is supported now. Aggregated reports contribute only the +normalize LENS and pVACseq; [native Exacto tables](exacto.md) use `read_exacto`. +Already normalized ORF/RNA DataFrames are also supported. Aggregated reports contribute only the candidates they actually report. A single input needs no model name, version or per-row source metadata. For diff --git a/docs/exacto.md b/docs/exacto.md new file mode 100644 index 0000000..4f55159 --- /dev/null +++ b/docs/exacto.md @@ -0,0 +1,124 @@ +# Reading native Exacto output + +`read_exacto` imports native Exacto TSV files into `TopiaryResult` without +running Exacto, reconstructing reads or executing a prediction model. Supply +`sample_name`: these files do not identify the patient/sample themselves. + +```python +from topiary import read_exacto + +exacto = read_exacto( + "sample_exacto_peptide_variants.tsv", + sample_name="patient-01", + primary_structures="sample_exacto_primary_structures.tsv", + tag="exacto-run-01", +) +``` + +## Supported native schemas + +The tested producer is [Exacto 0.4.6, commit +307c086](https://github.com/pirl-unc/exacto/tree/307c08670d5e706734bddf393bcebc84db497f9f). +Topiary identifies required column sets rather than assuming that a filename +or the producer's package version establishes a schema. `EXACTO_SCHEMAS` +exports these column sets; `schema=` can select one explicitly. Input may be a +path, gzip-compressed path or open text stream. Extra columns and original +records remain in `result.extra["exacto"]`, including companion tables. + +| Schema | Native output | Normalized observations | +| --- | --- | --- | +| `peptide_variants` | `call-peptide-vars` TSV | Reported peptide sequences and parent IDs; optional primary structures supply exact occurrences and context | +| `primary_structures` | `translate-structs` TSV | One translated ORF hypothesis per native peptide ID, with producer-annotated changed intervals | +| `translations` | `translate-seqs` TSV/TSV.gz | Every reported RNA/ORF translation, including partial alternatives | + +`transcript_read_support` is a companion table, supplied with the argument of +that name. It is accepted with primary structures, or peptide variants plus +primary structures. Provide `library_id` and `read_set_id`; stream inputs also +require a `tag` identifying the Exacto run. Local transcript model IDs are +scoped by this tag, or by the input path. Use the same run tag when importing +different files from one run. Distinct read names supply a transcript-level +read count with explicit membership. Missing models remain unknown. These +counts are not variant support or ORF-specific abundance; repeated peptide +rows do not create independent RNA observations. + +The native corpus in `tests/data/exacto` pins source paths and SHA-256 digests: +228 peptide records, six primary structures and 77 translations. Unsupported +headers, primary record types, sequence-bearing event rows, invalid codons or +inconsistent peptide/parent geometry raise `ValueError`. This reader does not +import arbitrary Exacto tables or reconstruct genomic events from local IDs. + +## What the evidence means + +Native DNA and RNA call IDs, transcript model IDs, reference transcript IDs and +all source records are retained. Local numeric IDs do not establish agreement +with another caller's genomic events. Translation ORF bounds are converted from +zero-based inclusive coordinates to zero-based half-open coordinates; original +values remain in metadata. Translation IDs include both RNA and peptide IDs, +since the producer reuses peptide IDs across RNA records. + +With primary structures, peptide coordinates and flanks are checked against +the reconstructed translation. Primary indices count base and event records, +so they are not treated as amino-acid coordinates. Changed amino-acid intervals +come from Exacto's explicit `amino_acid_change` labels. Without primary +structures, context and novelty intervals remain unknown and the reported +peptide is still available. + +`sequence_source="predicted_from_observed_rna"` distinguishes inferred protein +sequence from a protein-expression measurement. A complete `protein_sequence` +requires a start codon and terminal stop. Partial translations remain in +`protein_hypothesis_sequence`. Native files do not establish matched-normal +specificity or comparator protein sequences: these stay unknown. A changed +sequence is not automatically tumor-specific. + +## Combine with reported candidates + +```python +from topiary import ( + combine_sources, evidence_views, melt_pvacseq_algorithms, rank_candidates, + read_lens, read_pvacseq, reconcile_evidence, +) + +combined = reconcile_evidence(combine_sources({ + "exacto": exacto, + "lens": read_lens("lens.tsv"), + "pvacseq": melt_pvacseq_algorithms(read_pvacseq("all_epitopes.tsv")), +}, sample_name="patient-01")) +ranked = rank_candidates( + combined, "affinity['netmhcpan'].value", ascending=True, duplicates="best", +) +by_source = rank_candidates( + combined, "affinity['netmhcpan'].value", ascending=True, duplicates="best", + strata=["source_label", "candidate_mhc_class"], +) +combined.to_tsv("combined-evidence.tsv") +links = evidence_views(combined)["candidate_occurrences"] +``` + +Exacto's native files contain no HLA assignments or pMHC predictions. Therefore +its rows retain null `allele`, `value` and `candidate_id`; ORF-only rows also +have no peptide. The ranking universe comes from already reported pMHCs. +`candidate_occurrences` links same-sample, identical peptide occurrences to +those queries, with `reported_candidate=False` for a sequence match. This does +not transfer expression, scores or eligibility to a different observation. +All source records and native metadata survive long/wide CSV and TSV. + +Choose compatible original measurements explicitly. [Combined-source +ranking](combined-sources.md) explains conflicts, missing scores and additive +`rescore_candidates` calls; rescoring alone does not invent HLA combinations. + +## Optional new windows + +`read_exacto_fragments(path, **kwargs)` accepts the same inputs and produces +`ProteinFragment` records with the recovered sequence, novelty intervals and +native provenance. It calls no model. Empty native tables return an empty list. + +Pass these fragments to `TopiaryPredictor.predict_from_fragments` to explicitly +scan new peptide windows. This changes the candidate universe and is separate +from rescoring reported candidates. Select lengths/alleles deliberately and +use `overlaps_target` to filter recovered changed intervals. Missing intervals +remain unknown. Fragment conversion preserves each native observation, so +several reported peptides from one parent may carry the same parent sequence. + +The general reader uses no Varcode fusion reconstruction: that adapter handles +selected DNA-SV-linked linear RNA models, whereas these native translated +sequences can be imported directly without genomic anchors or raw reads. diff --git a/docs/fragments.md b/docs/fragments.md index 3f68fca..e5f1da0 100644 --- a/docs/fragments.md +++ b/docs/fragments.md @@ -467,7 +467,7 @@ Prefix is sanitized to `[A-Za-z0-9._:-]`; runs of other characters collapse to ` - **Indel / frameshift `wt_peptide`** — `wt_peptide` is only populated when the baseline is the same length as the mutant sequence (substitution-compatible). Length-changing edits yield `None`. Whether to define a remapped comparator remains an open design question ([#411](https://github.com/openvax/topiary/issues/411)). - **Binding-aware cross-reactivity axes** (`self_mimic_*`, `self_strongest_nearby_*`, `self_nearest_candidates`) — the sequence-level `self_nearest_*` columns are computed by `SelfProteome` / `predict_self_nearest`; the axes that also require MHC prediction on each candidate are not implemented ([#412](https://github.com/openvax/topiary/issues/412)). -- **Dedicated file loaders** (`read_isovar_fragments`, - `read_exacto_fragments`) — separate work. Existing in-memory results already - compose through `fragment_from_isovar_result` and - `fragments_from_dataframe(read_pvacseq(...).df)`. +- **Dedicated Isovar fragment-file loader** (`read_isovar_fragments`) — separate + work. Existing in-memory results compose through `fragment_from_isovar_result`. + [Native Exacto](exacto.md) now has `read_exacto_fragments`; pVACseq composes + through `fragments_from_dataframe(read_pvacseq(...).df)`. diff --git a/mkdocs.yml b/mkdocs.yml index f13ad8b..edb3def 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -19,6 +19,7 @@ nav: - Protein Fragments: fragments.md - Cached Predictions: cached.md - Reading pVACseq: pvacseq.md + - Reading Exacto: exacto.md - Combining Sources: combined-sources.md - Consumer Guide: consumer-guide.md - Cache Miss Reports: cache-miss-reporting.md diff --git a/tests/data/exacto/LICENSE b/tests/data/exacto/LICENSE new file mode 100644 index 0000000..8dada3e --- /dev/null +++ b/tests/data/exacto/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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+mutant_peptide_id peptide_id mutant_peptide_sequence k primary_structure_index_start primary_structure_index_end rna_variant_call_ids dna_variant_call_ids +0 1 NSSCMGGI 8 719 742 +1 1 SSCMGGIN 8 722 745 +2 1 SCMGGINR 8 725 748 +3 1 CMGGINRR 8 728 751 +4 1 MGGINRRP 8 731 754 +5 1 GGINRRPI 8 734 757 +6 1 GINRRPIL 8 737 760 +7 1 INRRPILT 8 740 763 +0 2 NSSCMGGI 8 719 742 +1 2 SSCMGGIN 8 722 745 +2 2 SCMGGINR 8 725 748 +3 2 CMGGINRR 8 728 751 +4 2 MGGINRRP 8 731 754 +5 2 GGINRRPI 8 734 757 +6 2 GINRRPIL 8 737 760 +7 2 INRRPILT 8 740 763 +0 3 NSSCMGGI 8 719 742 +1 3 SSCMGGIN 8 722 745 +2 3 SCMGGINR 8 725 748 +3 3 CMGGINRR 8 728 751 +4 3 MGGINRRP 8 731 754 +5 3 GGINRRPI 8 734 757 +6 3 GINRRPIL 8 737 760 +7 3 INRRPILT 8 740 763 +0 4 NSSCMGGI 8 719 742 +1 4 SSCMGGIN 8 722 745 +2 4 SCMGGINR 8 725 748 +3 4 CMGGINRR 8 728 751 +4 4 MGGINRRP 8 731 754 +5 4 GGINRRPI 8 734 757 +6 4 GINRRPIL 8 737 760 +7 4 INRRPILT 8 740 763 +0 5 NSSCMGGI 8 719 742 +1 5 SSCMGGIN 8 722 745 +2 5 SCMGGINR 8 725 748 +3 5 CMGGINRR 8 728 751 +4 5 MGGINRRP 8 731 754 +5 5 GGINRRPI 8 734 757 +6 5 GINRRPIL 8 737 760 +7 5 INRRPILT 8 740 763 +0 6 NSSCMGGI 8 719 742 +1 6 SSCMGGIN 8 722 745 +2 6 SCMGGINR 8 725 748 +3 6 CMGGINRR 8 728 751 +4 6 MGGINRRP 8 731 754 +5 6 GGINRRPI 8 734 757 +6 6 GINRRPIL 8 737 760 +7 6 INRRPILT 8 740 763 +8 1 CNSSCMGGI 9 716 742 +9 1 NSSCMGGIN 9 719 745 +10 1 SSCMGGINR 9 722 748 +11 1 SCMGGINRR 9 725 751 +12 1 CMGGINRRP 9 728 754 +13 1 MGGINRRPI 9 731 757 +14 1 GGINRRPIL 9 734 760 +15 1 GINRRPILT 9 737 763 +16 1 INRRPILTI 9 740 766 +8 2 CNSSCMGGI 9 716 742 +9 2 NSSCMGGIN 9 719 745 +10 2 SSCMGGINR 9 722 748 +11 2 SCMGGINRR 9 725 751 +12 2 CMGGINRRP 9 728 754 +13 2 MGGINRRPI 9 731 757 +14 2 GGINRRPIL 9 734 760 +15 2 GINRRPILT 9 737 763 +16 2 INRRPILTI 9 740 766 +8 3 CNSSCMGGI 9 716 742 +9 3 NSSCMGGIN 9 719 745 +10 3 SSCMGGINR 9 722 748 +11 3 SCMGGINRR 9 725 751 +12 3 CMGGINRRP 9 728 754 +13 3 MGGINRRPI 9 731 757 +14 3 GGINRRPIL 9 734 760 +15 3 GINRRPILT 9 737 763 +16 3 INRRPILTI 9 740 766 +8 4 CNSSCMGGI 9 716 742 +9 4 NSSCMGGIN 9 719 745 +10 4 SSCMGGINR 9 722 748 +11 4 SCMGGINRR 9 725 751 +12 4 CMGGINRRP 9 728 754 +13 4 MGGINRRPI 9 731 757 +14 4 GGINRRPIL 9 734 760 +15 4 GINRRPILT 9 737 763 +16 4 INRRPILTI 9 740 766 +8 5 CNSSCMGGI 9 716 742 +9 5 NSSCMGGIN 9 719 745 +10 5 SSCMGGINR 9 722 748 +11 5 SCMGGINRR 9 725 751 +12 5 CMGGINRRP 9 728 754 +13 5 MGGINRRPI 9 731 757 +14 5 GGINRRPIL 9 734 760 +15 5 GINRRPILT 9 737 763 +16 5 INRRPILTI 9 740 766 +8 6 CNSSCMGGI 9 716 742 +9 6 NSSCMGGIN 9 719 745 +10 6 SSCMGGINR 9 722 748 +11 6 SCMGGINRR 9 725 751 +12 6 CMGGINRRP 9 728 754 +13 6 MGGINRRPI 9 731 757 +14 6 GGINRRPIL 9 734 760 +15 6 GINRRPILT 9 737 763 +16 6 INRRPILTI 9 740 766 +17 1 MCNSSCMGGI 10 713 742 +18 1 CNSSCMGGIN 10 716 745 +19 1 NSSCMGGINR 10 719 748 +20 1 SSCMGGINRR 10 722 751 +21 1 SCMGGINRRP 10 725 754 +22 1 CMGGINRRPI 10 728 757 +23 1 MGGINRRPIL 10 731 760 +24 1 GGINRRPILT 10 734 763 +25 1 GINRRPILTI 10 737 766 +26 1 INRRPILTII 10 740 769 +17 2 MCNSSCMGGI 10 713 742 +18 2 CNSSCMGGIN 10 716 745 +19 2 NSSCMGGINR 10 719 748 +20 2 SSCMGGINRR 10 722 751 +21 2 SCMGGINRRP 10 725 754 +22 2 CMGGINRRPI 10 728 757 +23 2 MGGINRRPIL 10 731 760 +24 2 GGINRRPILT 10 734 763 +25 2 GINRRPILTI 10 737 766 +26 2 INRRPILTII 10 740 769 +17 3 MCNSSCMGGI 10 713 742 +18 3 CNSSCMGGIN 10 716 745 +19 3 NSSCMGGINR 10 719 748 +20 3 SSCMGGINRR 10 722 751 +21 3 SCMGGINRRP 10 725 754 +22 3 CMGGINRRPI 10 728 757 +23 3 MGGINRRPIL 10 731 760 +24 3 GGINRRPILT 10 734 763 +25 3 GINRRPILTI 10 737 766 +26 3 INRRPILTII 10 740 769 +17 4 MCNSSCMGGI 10 713 742 +18 4 CNSSCMGGIN 10 716 745 +19 4 NSSCMGGINR 10 719 748 +20 4 SSCMGGINRR 10 722 751 +21 4 SCMGGINRRP 10 725 754 +22 4 CMGGINRRPI 10 728 757 +23 4 MGGINRRPIL 10 731 760 +24 4 GGINRRPILT 10 734 763 +25 4 GINRRPILTI 10 737 766 +26 4 INRRPILTII 10 740 769 +17 5 MCNSSCMGGI 10 713 742 +18 5 CNSSCMGGIN 10 716 745 +19 5 NSSCMGGINR 10 719 748 +20 5 SSCMGGINRR 10 722 751 +21 5 SCMGGINRRP 10 725 754 +22 5 CMGGINRRPI 10 728 757 +23 5 MGGINRRPIL 10 731 760 +24 5 GGINRRPILT 10 734 763 +25 5 GINRRPILTI 10 737 766 +26 5 INRRPILTII 10 740 769 +17 6 MCNSSCMGGI 10 713 742 +18 6 CNSSCMGGIN 10 716 745 +19 6 NSSCMGGINR 10 719 748 +20 6 SSCMGGINRR 10 722 751 +21 6 SCMGGINRRP 10 725 754 +22 6 CMGGINRRPI 10 728 757 +23 6 MGGINRRPIL 10 731 760 +24 6 GGINRRPILT 10 734 763 +25 6 GINRRPILTI 10 737 766 +26 6 INRRPILTII 10 740 769 +27 1 YMCNSSCMGGI 11 710 742 +28 1 MCNSSCMGGIN 11 713 745 +29 1 CNSSCMGGINR 11 716 748 +30 1 NSSCMGGINRR 11 719 751 +31 1 SSCMGGINRRP 11 722 754 +32 1 SCMGGINRRPI 11 725 757 +33 1 CMGGINRRPIL 11 728 760 +34 1 MGGINRRPILT 11 731 763 +35 1 GGINRRPILTI 11 734 766 +36 1 GINRRPILTII 11 737 769 +37 1 INRRPILTIIT 11 740 772 +27 2 YMCNSSCMGGI 11 710 742 +28 2 MCNSSCMGGIN 11 713 745 +29 2 CNSSCMGGINR 11 716 748 +30 2 NSSCMGGINRR 11 719 751 +31 2 SSCMGGINRRP 11 722 754 +32 2 SCMGGINRRPI 11 725 757 +33 2 CMGGINRRPIL 11 728 760 +34 2 MGGINRRPILT 11 731 763 +35 2 GGINRRPILTI 11 734 766 +36 2 GINRRPILTII 11 737 769 +37 2 INRRPILTIIT 11 740 772 +27 3 YMCNSSCMGGI 11 710 742 +28 3 MCNSSCMGGIN 11 713 745 +29 3 CNSSCMGGINR 11 716 748 +30 3 NSSCMGGINRR 11 719 751 +31 3 SSCMGGINRRP 11 722 754 +32 3 SCMGGINRRPI 11 725 757 +33 3 CMGGINRRPIL 11 728 760 +34 3 MGGINRRPILT 11 731 763 +35 3 GGINRRPILTI 11 734 766 +36 3 GINRRPILTII 11 737 769 +37 3 INRRPILTIIT 11 740 772 +27 4 YMCNSSCMGGI 11 710 742 +28 4 MCNSSCMGGIN 11 713 745 +29 4 CNSSCMGGINR 11 716 748 +30 4 NSSCMGGINRR 11 719 751 +31 4 SSCMGGINRRP 11 722 754 +32 4 SCMGGINRRPI 11 725 757 +33 4 CMGGINRRPIL 11 728 760 +34 4 MGGINRRPILT 11 731 763 +35 4 GGINRRPILTI 11 734 766 +36 4 GINRRPILTII 11 737 769 +37 4 INRRPILTIIT 11 740 772 +27 5 YMCNSSCMGGI 11 710 742 +28 5 MCNSSCMGGIN 11 713 745 +29 5 CNSSCMGGINR 11 716 748 +30 5 NSSCMGGINRR 11 719 751 +31 5 SSCMGGINRRP 11 722 754 +32 5 SCMGGINRRPI 11 725 757 +33 5 CMGGINRRPIL 11 728 760 +34 5 MGGINRRPILT 11 731 763 +35 5 GGINRRPILTI 11 734 766 +36 5 GINRRPILTII 11 737 769 +37 5 INRRPILTIIT 11 740 772 +27 6 YMCNSSCMGGI 11 710 742 +28 6 MCNSSCMGGIN 11 713 745 +29 6 CNSSCMGGINR 11 716 748 +30 6 NSSCMGGINRR 11 719 751 +31 6 SSCMGGINRRP 11 722 754 +32 6 SCMGGINRRPI 11 725 757 +33 6 CMGGINRRPIL 11 728 760 +34 6 MGGINRRPILT 11 731 763 +35 6 GGINRRPILTI 11 734 766 +36 6 GINRRPILTII 11 737 769 +37 6 INRRPILTIIT 11 740 772 diff --git a/tests/data/exacto/primary-structures.tsv b/tests/data/exacto/primary-structures.tsv new file mode 100644 index 0000000..73797a1 --- /dev/null +++ b/tests/data/exacto/primary-structures.tsv @@ -0,0 +1,7147 @@ +peptide_id primary_structure_index type amino_acid amino_acid_index codon_index nucleotide transcript_model_id reference_transcript_ids transcript_structure_index read_start read_end net_variant_nucleotides_count frameshift_state rna_variant_call_ids dna_variant_call_ids codon_rna_variant_call_ids codon_dna_variant_call_ids frameshift_rna_variant_call_ids frameshift_dna_variant_call_ids amino_acid_change +1 0 base M 0 0 a 1 ENST00000269305.9 2 142 142 0 inframe "" "" "" "" "" "" reference +1 1 base M 0 1 t 1 ENST00000269305.9 2 143 143 0 inframe "" "" "" "" "" "" reference +1 2 base M 0 2 g 1 ENST00000269305.9 2 144 144 0 inframe "" "" "" "" "" "" reference +1 3 base E 1 0 g 1 ENST00000269305.9 2 145 145 0 inframe "" "" "" "" "" "" reference +1 4 base E 1 1 a 1 ENST00000269305.9 2 146 146 0 inframe "" "" "" "" "" "" reference +1 5 base E 1 2 g 1 ENST00000269305.9 2 147 147 0 inframe "" "" "" "" "" "" reference +1 6 base E 2 0 g 1 ENST00000269305.9 2 148 148 0 inframe "" "" "" "" "" "" reference +1 7 base E 2 1 a 1 ENST00000269305.9 2 149 149 0 inframe "" "" "" "" "" "" reference +1 8 base E 2 2 g 1 ENST00000269305.9 2 150 150 0 inframe "" "" "" "" "" "" reference +1 9 base P 3 0 c 1 ENST00000269305.9 2 151 151 0 inframe "" "" "" "" "" "" reference +1 10 base P 3 1 c 1 ENST00000269305.9 2 152 152 0 inframe "" "" "" "" "" "" reference +1 11 base P 3 2 g 1 ENST00000269305.9 2 153 153 0 inframe "" "" "" "" "" "" reference +1 12 base Q 4 0 c 1 ENST00000269305.9 2 154 154 0 inframe "" "" "" "" "" "" reference +1 13 base Q 4 1 a 1 ENST00000269305.9 2 155 155 0 inframe "" "" "" "" "" "" reference +1 14 base Q 4 2 g 1 ENST00000269305.9 2 156 156 0 inframe "" "" "" "" "" "" reference +1 15 base S 5 0 t 1 ENST00000269305.9 2 157 157 0 inframe "" "" "" "" "" "" reference +1 16 base S 5 1 c 1 ENST00000269305.9 2 158 158 0 inframe "" "" "" "" "" "" reference +1 17 base S 5 2 a 1 ENST00000269305.9 2 159 159 0 inframe "" "" "" "" "" "" reference +1 18 base D 6 0 g 1 ENST00000269305.9 2 160 160 0 inframe "" "" "" "" "" "" reference +1 19 base D 6 1 a 1 ENST00000269305.9 2 161 161 0 inframe "" "" "" "" "" "" reference +1 20 base D 6 2 t 1 ENST00000269305.9 2 162 162 0 inframe "" "" "" "" "" "" reference +1 21 base P 7 0 c 1 ENST00000269305.9 2 163 163 0 inframe "" "" "" "" "" "" reference +1 22 base P 7 1 c 1 ENST00000269305.9 2 164 164 0 inframe "" "" "" "" "" "" reference +1 23 base P 7 2 t 1 ENST00000269305.9 2 165 165 0 inframe "" "" "" "" "" "" reference +1 24 base S 8 0 a 1 ENST00000269305.9 2 166 166 0 inframe "" "" "" "" "" "" reference +1 25 base S 8 1 g 1 ENST00000269305.9 2 167 167 0 inframe "" "" "" "" "" "" reference +1 26 base S 8 2 c 1 ENST00000269305.9 2 168 168 0 inframe "" "" "" "" "" "" reference +1 27 base V 9 0 g 1 ENST00000269305.9 2 169 169 0 inframe "" "" "" "" "" "" reference +1 28 base V 9 1 t 1 ENST00000269305.9 2 170 170 0 inframe "" "" "" "" "" "" reference +1 29 base V 9 2 c 1 ENST00000269305.9 2 171 171 0 inframe "" "" "" "" "" "" reference +1 30 base E 10 0 g 1 ENST00000269305.9 2 172 172 0 inframe "" "" "" "" "" "" reference +1 31 base E 10 1 a 1 ENST00000269305.9 2 173 173 0 inframe "" "" "" "" "" "" reference +1 32 base E 10 2 g 1 ENST00000269305.9 2 174 174 0 inframe "" "" "" "" "" "" reference +1 33 base P 11 0 c 1 ENST00000269305.9 2 175 175 0 inframe "" "" "" "" "" "" reference +1 34 base P 11 1 c 1 ENST00000269305.9 2 176 176 0 inframe "" "" "" "" "" "" reference +1 35 base P 11 2 c 1 ENST00000269305.9 2 177 177 0 inframe "" "" "" "" "" "" reference +1 36 base P 12 0 c 1 ENST00000269305.9 2 178 178 0 inframe "" "" "" "" "" "" reference +1 37 base P 12 1 c 1 ENST00000269305.9 2 179 179 0 inframe "" "" "" "" "" "" reference +1 38 base P 12 2 t 1 ENST00000269305.9 2 180 180 0 inframe "" "" "" "" "" "" reference +1 39 base L 13 0 c 1 ENST00000269305.9 2 181 181 0 inframe "" "" "" "" "" "" reference +1 40 base L 13 1 t 1 ENST00000269305.9 2 182 182 0 inframe "" "" "" "" "" "" reference +1 41 base L 13 2 g 1 ENST00000269305.9 2 183 183 0 inframe "" "" "" "" "" "" reference +1 42 base S 14 0 a 1 ENST00000269305.9 2 184 184 0 inframe "" "" "" "" "" "" reference +1 43 base S 14 1 g 1 ENST00000269305.9 2 185 185 0 inframe "" "" "" "" "" "" reference +1 44 base S 14 2 t 1 ENST00000269305.9 2 186 186 0 inframe "" "" "" "" "" "" reference +1 45 base Q 15 0 c 1 ENST00000269305.9 2 187 187 0 inframe "" "" "" "" "" "" reference +1 46 base Q 15 1 a 1 ENST00000269305.9 2 188 188 0 inframe "" "" "" "" "" "" reference +1 47 base Q 15 2 g 1 ENST00000269305.9 2 189 189 0 inframe "" "" "" "" "" "" reference +1 48 base E 16 0 g 1 ENST00000269305.9 2 190 190 0 inframe "" "" "" "" "" "" reference +1 49 base E 16 1 a 1 ENST00000269305.9 2 191 191 0 inframe "" "" "" "" "" "" reference +1 50 base E 16 2 a 1 ENST00000269305.9 2 192 192 0 inframe "" "" "" "" "" "" reference +1 51 base T 17 0 a 1 ENST00000269305.9 2 193 193 0 inframe "" "" "" "" "" "" reference +1 52 base T 17 1 c 1 ENST00000269305.9 2 194 194 0 inframe "" "" "" "" "" "" reference +1 53 base T 17 2 a 1 ENST00000269305.9 2 195 195 0 inframe "" "" "" "" "" "" reference +1 54 base F 18 0 t 1 ENST00000269305.9 2 196 196 0 inframe "" "" "" "" "" "" reference +1 55 base F 18 1 t 1 ENST00000269305.9 2 197 197 0 inframe "" "" "" "" "" "" reference +1 56 base F 18 2 t 1 ENST00000269305.9 2 198 198 0 inframe "" "" "" "" "" "" reference +1 57 base S 19 0 t 1 ENST00000269305.9 2 199 199 0 inframe "" "" "" "" "" "" reference +1 58 base S 19 1 c 1 ENST00000269305.9 2 200 200 0 inframe "" "" "" "" "" "" reference +1 59 base S 19 2 a 1 ENST00000269305.9 2 201 201 0 inframe "" "" "" "" "" "" reference +1 60 base D 20 0 g 1 ENST00000269305.9 2 202 202 0 inframe "" "" "" "" "" "" reference +1 61 base D 20 1 a 1 ENST00000269305.9 2 203 203 0 inframe "" "" "" "" "" "" reference +1 62 base D 20 2 c 1 ENST00000269305.9 2 204 204 0 inframe "" "" "" "" "" "" reference +1 63 base L 21 0 c 1 ENST00000269305.9 2 205 205 0 inframe "" "" "" "" "" "" reference +1 64 base L 21 1 t 1 ENST00000269305.9 2 206 206 0 inframe "" "" "" "" "" "" reference +1 65 base L 21 2 a 1 ENST00000269305.9 2 207 207 0 inframe "" "" "" "" "" "" reference +1 66 base W 22 0 t 1 ENST00000269305.9 2 208 208 0 inframe "" "" "" "" "" "" reference +1 67 base W 22 1 g 1 ENST00000269305.9 2 209 209 0 inframe "" "" "" "" "" "" reference +1 68 base W 22 2 g 1 ENST00000269305.9 2 210 210 0 inframe "" "" "" "" "" "" reference +1 69 base K 23 0 a 1 ENST00000269305.9 2 211 211 0 inframe "" "" "" "" "" "" reference +1 70 base K 23 1 a 1 ENST00000269305.9 2 212 212 0 inframe "" "" "" "" "" "" reference +1 71 base K 23 2 a 1 ENST00000269305.9 2 213 213 0 inframe "" "" "" "" "" "" reference +1 72 base L 24 0 c 1 ENST00000269305.9 2 214 214 0 inframe "" "" "" "" "" "" reference +1 73 base L 24 1 t 1 ENST00000269305.9 2 215 215 0 inframe "" "" "" "" "" "" reference +1 74 event "" -1 -1 "" 1 ENST00000269305.9 3 215 216 0 "" "" "" "" "" "" "" "" +1 75 base L 24 2 a 1 ENST00000269305.9 4 216 216 0 inframe "" "" "" "" "" "" reference +1 76 base L 25 0 c 1 ENST00000269305.9 4 217 217 0 inframe "" "" "" "" "" "" reference +1 77 base L 25 1 t 1 ENST00000269305.9 4 218 218 0 inframe "" "" "" "" "" "" reference +1 78 base L 25 2 t 1 ENST00000269305.9 4 219 219 0 inframe "" "" "" "" "" "" reference +1 79 base P 26 0 c 1 ENST00000269305.9 4 220 220 0 inframe "" "" "" "" "" "" reference +1 80 base P 26 1 c 1 ENST00000269305.9 4 221 221 0 inframe "" "" "" "" "" "" reference +1 81 base P 26 2 t 1 ENST00000269305.9 4 222 222 0 inframe "" "" "" "" "" "" reference +1 82 base E 27 0 g 1 ENST00000269305.9 4 223 223 0 inframe "" "" "" "" "" "" reference +1 83 base E 27 1 a 1 ENST00000269305.9 4 224 224 0 inframe "" "" "" "" "" "" reference +1 84 base E 27 2 a 1 ENST00000269305.9 4 225 225 0 inframe "" "" "" "" "" "" reference +1 85 base N 28 0 a 1 ENST00000269305.9 4 226 226 0 inframe "" "" "" "" "" "" reference +1 86 base N 28 1 a 1 ENST00000269305.9 4 227 227 0 inframe "" "" "" "" "" "" reference +1 87 base N 28 2 c 1 ENST00000269305.9 4 228 228 0 inframe "" "" "" "" "" "" reference +1 88 base N 29 0 a 1 ENST00000269305.9 4 229 229 0 inframe "" "" "" "" "" "" reference +1 89 base N 29 1 a 1 ENST00000269305.9 4 230 230 0 inframe "" "" "" "" "" "" reference +1 90 base N 29 2 c 1 ENST00000269305.9 4 231 231 0 inframe "" "" "" "" "" "" reference +1 91 base V 30 0 g 1 ENST00000269305.9 4 232 232 0 inframe "" "" "" "" "" "" reference +1 92 base V 30 1 t 1 ENST00000269305.9 4 233 233 0 inframe "" "" "" "" "" "" reference +1 93 base V 30 2 t 1 ENST00000269305.9 4 234 234 0 inframe "" "" "" "" "" "" reference +1 94 base L 31 0 c 1 ENST00000269305.9 4 235 235 0 inframe "" "" "" "" "" "" reference +1 95 base L 31 1 t 1 ENST00000269305.9 4 236 236 0 inframe "" "" "" "" "" "" reference +1 96 base L 31 2 g 1 ENST00000269305.9 4 237 237 0 inframe "" "" "" "" "" "" reference +1 97 event "" -1 -1 "" 1 ENST00000269305.9 5 237 238 0 "" "" "" "" "" "" "" "" +1 98 base S 32 0 t 1 ENST00000269305.9 6 238 238 0 inframe "" "" "" "" "" "" reference +1 99 base S 32 1 c 1 ENST00000269305.9 6 239 239 0 inframe "" "" "" "" "" "" reference +1 100 base S 32 2 c 1 ENST00000269305.9 6 240 240 0 inframe "" "" "" "" "" "" reference +1 101 base P 33 0 c 1 ENST00000269305.9 6 241 241 0 inframe "" "" "" "" "" "" reference +1 102 base P 33 1 c 1 ENST00000269305.9 6 242 242 0 inframe "" "" "" "" "" "" reference +1 103 base P 33 2 c 1 ENST00000269305.9 6 243 243 0 inframe "" "" "" "" "" "" reference +1 104 base L 34 0 t 1 ENST00000269305.9 6 244 244 0 inframe "" "" "" "" "" "" reference +1 105 base L 34 1 t 1 ENST00000269305.9 6 245 245 0 inframe "" "" "" "" "" "" reference +1 106 base L 34 2 g 1 ENST00000269305.9 6 246 246 0 inframe "" "" "" "" "" "" reference +1 107 base P 35 0 c 1 ENST00000269305.9 6 247 247 0 inframe "" "" "" "" "" "" reference +1 108 base P 35 1 c 1 ENST00000269305.9 6 248 248 0 inframe "" "" "" "" "" "" reference +1 109 base P 35 2 g 1 ENST00000269305.9 6 249 249 0 inframe "" "" "" "" "" "" reference +1 110 base S 36 0 t 1 ENST00000269305.9 6 250 250 0 inframe "" "" "" "" "" "" reference +1 111 base S 36 1 c 1 ENST00000269305.9 6 251 251 0 inframe "" "" "" "" "" "" reference +1 112 base S 36 2 c 1 ENST00000269305.9 6 252 252 0 inframe "" "" "" "" "" "" reference +1 113 base Q 37 0 c 1 ENST00000269305.9 6 253 253 0 inframe "" "" "" "" "" "" reference +1 114 base Q 37 1 a 1 ENST00000269305.9 6 254 254 0 inframe "" "" "" "" "" "" reference +1 115 base Q 37 2 a 1 ENST00000269305.9 6 255 255 0 inframe "" "" "" "" "" "" reference +1 116 base A 38 0 g 1 ENST00000269305.9 6 256 256 0 inframe "" "" "" "" "" "" reference +1 117 base A 38 1 c 1 ENST00000269305.9 6 257 257 0 inframe "" "" "" "" "" "" reference +1 118 base A 38 2 a 1 ENST00000269305.9 6 258 258 0 inframe "" "" "" "" "" "" reference +1 119 base M 39 0 a 1 ENST00000269305.9 6 259 259 0 inframe "" "" "" "" "" "" reference +1 120 base M 39 1 t 1 ENST00000269305.9 6 260 260 0 inframe "" "" "" "" "" "" reference +1 121 base M 39 2 g 1 ENST00000269305.9 6 261 261 0 inframe "" "" "" "" "" "" reference +1 122 base D 40 0 g 1 ENST00000269305.9 6 262 262 0 inframe "" "" "" "" "" "" reference +1 123 base D 40 1 a 1 ENST00000269305.9 6 263 263 0 inframe "" "" "" "" "" "" reference +1 124 base D 40 2 t 1 ENST00000269305.9 6 264 264 0 inframe "" "" "" "" "" "" reference +1 125 base D 41 0 g 1 ENST00000269305.9 6 265 265 0 inframe "" "" "" "" "" "" reference +1 126 base D 41 1 a 1 ENST00000269305.9 6 266 266 0 inframe "" "" "" "" "" "" reference +1 127 base D 41 2 t 1 ENST00000269305.9 6 267 267 0 inframe "" "" "" "" "" "" reference +1 128 base L 42 0 t 1 ENST00000269305.9 6 268 268 0 inframe "" "" "" "" "" "" reference +1 129 base L 42 1 t 1 ENST00000269305.9 6 269 269 0 inframe "" "" "" "" "" "" reference +1 130 base L 42 2 g 1 ENST00000269305.9 6 270 270 0 inframe "" "" "" "" "" "" reference +1 131 base M 43 0 a 1 ENST00000269305.9 6 271 271 0 inframe "" "" "" "" "" "" reference +1 132 base M 43 1 t 1 ENST00000269305.9 6 272 272 0 inframe "" "" "" "" "" "" reference +1 133 base M 43 2 g 1 ENST00000269305.9 6 273 273 0 inframe "" "" "" "" "" "" reference +1 134 base L 44 0 c 1 ENST00000269305.9 6 274 274 0 inframe "" "" "" "" "" "" reference +1 135 base L 44 1 t 1 ENST00000269305.9 6 275 275 0 inframe "" "" "" "" "" "" reference +1 136 base L 44 2 g 1 ENST00000269305.9 6 276 276 0 inframe "" "" "" "" "" "" reference +1 137 base S 45 0 t 1 ENST00000269305.9 6 277 277 0 inframe "" "" "" "" "" "" reference +1 138 base S 45 1 c 1 ENST00000269305.9 6 278 278 0 inframe "" "" "" "" "" "" reference +1 139 base S 45 2 c 1 ENST00000269305.9 6 279 279 0 inframe "" "" "" "" "" "" reference +1 140 base P 46 0 c 1 ENST00000269305.9 6 280 280 0 inframe "" "" "" "" "" "" reference +1 141 base P 46 1 c 1 ENST00000269305.9 6 281 281 0 inframe "" "" "" "" "" "" reference +1 142 base P 46 2 g 1 ENST00000269305.9 6 282 282 0 inframe "" "" "" "" "" "" reference +1 143 base D 47 0 g 1 ENST00000269305.9 6 283 283 0 inframe "" "" "" "" "" "" reference +1 144 base D 47 1 a 1 ENST00000269305.9 6 284 284 0 inframe "" "" "" "" "" "" reference +1 145 base D 47 2 c 1 ENST00000269305.9 6 285 285 0 inframe "" "" "" "" "" "" reference +1 146 base D 48 0 g 1 ENST00000269305.9 6 286 286 0 inframe "" "" "" "" "" "" reference +1 147 base D 48 1 a 1 ENST00000269305.9 6 287 287 0 inframe "" "" "" "" "" "" reference +1 148 base D 48 2 t 1 ENST00000269305.9 6 288 288 0 inframe "" "" "" "" "" "" reference +1 149 base I 49 0 a 1 ENST00000269305.9 6 289 289 0 inframe "" "" "" "" "" "" reference +1 150 base I 49 1 t 1 ENST00000269305.9 6 290 290 0 inframe "" "" "" "" "" "" reference +1 151 base I 49 2 t 1 ENST00000269305.9 6 291 291 0 inframe "" "" "" "" "" "" reference +1 152 base E 50 0 g 1 ENST00000269305.9 6 292 292 0 inframe "" "" "" "" "" "" reference +1 153 base E 50 1 a 1 ENST00000269305.9 6 293 293 0 inframe "" "" "" "" "" "" reference +1 154 base E 50 2 a 1 ENST00000269305.9 6 294 294 0 inframe "" "" "" "" "" "" reference +1 155 base Q 51 0 c 1 ENST00000269305.9 6 295 295 0 inframe "" "" "" "" "" "" reference +1 156 base Q 51 1 a 1 ENST00000269305.9 6 296 296 0 inframe "" "" "" "" "" "" reference +1 157 base Q 51 2 a 1 ENST00000269305.9 6 297 297 0 inframe "" "" "" "" "" "" reference +1 158 base W 52 0 t 1 ENST00000269305.9 6 298 298 0 inframe "" "" "" "" "" "" reference +1 159 base W 52 1 g 1 ENST00000269305.9 6 299 299 0 inframe "" "" "" "" "" "" reference +1 160 base W 52 2 g 1 ENST00000269305.9 6 300 300 0 inframe "" "" "" "" "" "" reference +1 161 base F 53 0 t 1 ENST00000269305.9 6 301 301 0 inframe "" "" "" "" "" "" reference +1 162 base F 53 1 t 1 ENST00000269305.9 6 302 302 0 inframe "" "" "" "" "" "" reference +1 163 base F 53 2 c 1 ENST00000269305.9 6 303 303 0 inframe "" "" "" "" "" "" reference +1 164 base T 54 0 a 1 ENST00000269305.9 6 304 304 0 inframe "" "" "" "" "" "" reference +1 165 base T 54 1 c 1 ENST00000269305.9 6 305 305 0 inframe "" "" "" "" "" "" reference +1 166 base T 54 2 t 1 ENST00000269305.9 6 306 306 0 inframe "" "" "" "" "" "" reference +1 167 base E 55 0 g 1 ENST00000269305.9 6 307 307 0 inframe "" "" "" "" "" "" reference +1 168 base E 55 1 a 1 ENST00000269305.9 6 308 308 0 inframe "" "" "" "" "" "" reference +1 169 base E 55 2 a 1 ENST00000269305.9 6 309 309 0 inframe "" "" "" "" "" "" reference +1 170 base D 56 0 g 1 ENST00000269305.9 6 310 310 0 inframe "" 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"examples/outputs/call-peptide-vars/rna-100-tumor_minimap2_mdtagged_sorted_exacto_peptide_variants.tsv", + "sha256": "90d5f285b386fc61af91d38daf2d062fb74e54911d38b562e1373366c3fc72a0" + }, + "primary-structures.tsv": { + "source": "examples/outputs/translate-structs/rna-100-tumor_minimap2_mdtagged_sorted_exacto_primary_structures.tsv", + "sha256": "6d4f210d06ee88eee8a10a4c74af4ba76921f0b5e1f24c5d5c0ac3a408e4c425" + }, + "translations.tsv.gz": { + "source": "examples/outputs/translate-seqs/sample_tumor_long_read_rna_exacto_translations_all-orfs.tsv.gz", + "sha256": "95cc819b6f12e8f92d30c797d535bd5aab1d4b176ff9aa0a39c18302c0310804" + }, + "transcript-read-support.tsv": { + "source": "examples/outputs/call-rna-vars/rna-100-tumor-minimap2_mdtagged_sorted_bam_exacto_call_rna_vars_outputs/rna-100-tumor_minimap2_mdtagged_sorted_exacto_transcripts_read_support.tsv", + "sha256": "0897b4e6f2c9294f4ec80d575dc6f2a853d7ce16636f45070abc148484998a89" + } + } +} diff --git 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zyw2OWIqXC4^@=F&$?o78z&ygqr1O0b$QFYM9*Nq~`s(3b80T*lkI>6oIS(&1+j#~W zy}GZRS6MjhDok*-CT6`_z=}j@BUjkf3-xy5`9_5!4)Q3rieUe|yl%-umw~FSW}OBA zb%Ad-78U>`wWFsNvCh9 end or end >= len(rna): + raise ValueError("Exacto ORF bounds exceed RNA sequence") + row.update(_protein(native_row["peptide_sequence"], rna[start:end + 1]), + orf_id="exacto:translation:" + _identity([native_row["rna_id"], identity]), + nucleotide_sequence=rna, orf_start=start, orf_end=end + 1, + reading_frame=start % 3, exacto_rna_id=native_row["rna_id"], exacto_record_id=identity) + else: + peptide = native_row["mutant_peptide_sequence"] + if not peptide or "*" in peptide or len(peptide) != _integer(native_row, "k"): + raise ValueError("Exacto peptide sequence disagrees with k") + start, end = (_integer(native_row, f"primary_structure_index_{side}") for side in ("start", "end")) + if start > end: + raise ValueError("Exacto primary interval is reversed") + row.update(peptide=peptide, sequence=peptide, exacto_record_id=native_row["mutant_peptide_id"]) + for assay in ("rna", "dna"): + row[f"exacto_{assay}_variant_call_ids"] = _ids(native_row[f"{assay}_variant_call_ids"]) + if primary_structures is not None: + if identity not in proteins: + raise ValueError(f"Missing Exacto primary structure for peptide_id {identity}") + parent, spans = proteins[identity] + if start not in spans or end not in spans: + raise ValueError("Exacto peptide interval does not name coding bases") + if spans[start][1] != 0 or spans[end][1] != 2: + raise ValueError("Exacto peptide interval must span complete codons") + peptide_start, peptide_end = spans[start][0], spans[end][0] + 1 + if parent["sequence"][peptide_start:peptide_end] != peptide: + raise ValueError("Exacto peptide disagrees with its primary structure") + row.update({k: deepcopy(v) for k, v in parent.items() if k not in + {"exacto_record_id", "exacto_native_rows", "exacto_rna_variant_call_ids", "exacto_dna_variant_call_ids"}}) + row.update(peptide_start=peptide_start, peptide_end=peptide_end, + n_flank=parent["sequence"][:peptide_start], c_flank=parent["sequence"][peptide_end:], + mutation_intervals_in_peptide=[[max(a, peptide_start) - peptide_start, + min(b, peptide_end) - peptide_start] + for a, b in parent["target_intervals"] + if a < peptide_end and b > peptide_start]) + rows.append(row) + for row in rows: + members = support.get(row.get("exacto_transcript_model_id")) + row["rna_observations"] = [] if members is None else [dict( + sample_name=sample_name, entity_type="transcript", + entity_id=f"exacto:{tag or provenance['file']}:{row['exacto_transcript_model_id']}", + quantity="count", unit="reads", value=len(members), evidence_unit_ids=sorted(members), + library_id=library_id, read_set_id=read_set_id, method="exacto_transcript_read_support")] + row.update(sample_name=sample_name, reference_name=reference_name, source_type="rna:translation", + sequence_source="predicted_from_observed_rna", tumor_specificity=None) + frame = pd.DataFrame(rows, columns=_COLUMNS) + return TopiaryResult(frame, sources=[tag or Path(provenance["file"]).name], form="long", + extra={"exacto": dict(provenance, tested_producer_commit=EXACTO_SCHEMA_COMMIT, + primary_structures=primary_provenance, transcript_read_support=support_provenance)}) + + +def read_exacto_fragments(path, **kwargs): + """Convert supported native Exacto rows into optional prediction fragments. + + Parameters + ---------- + path : path or text stream + Native table accepted by ``read_exacto``. + **kwargs + Passed unchanged to ``read_exacto``, including required ``sample_name``. + + Returns + ------- + list of ProteinFragment + Distinct source records with their translated sequence, exact recovered + novelty intervals (unknown without primary structures) and native evidence + provenance. No predictor runs. This is a separate, explicit precursor to + scanning new windows with ``TopiaryPredictor.predict_from_fragments``; + it does not rescore or modify the original reported-candidate universe. + Empty input returns an empty list. Missing comparator/specificity stays + unknown; target intervals indicate sequence change, not tumor specificity. + """ + result = read_exacto(path, **kwargs) + fragments = [] + for row in result.df.to_dict("records"): + # Each native occurrence remains distinct even for repeated sequences. + identity = _identity([result.sources, row["orf_id"], row["exacto_record_id"], row["exacto_native_rows"]]) + intervals = row["target_intervals"] if isinstance(row["target_intervals"], list) else None + provenance = result.extra["exacto"] + evidence = {k: deepcopy(v) for k, v in provenance.items() if k not in {"records", "primary_structures", "transcript_read_support"}} + evidence["records"] = [deepcopy(provenance["records"][i]) for i in row["exacto_native_rows"]] + primary = provenance.get("primary_structures") + if primary is not None: + evidence["primary_structures"] = { + "schema": primary["schema"], "file": primary["file"], "columns": primary["columns"], + "records": [deepcopy(primary["records"][i]) for i in row["exacto_primary_rows"]], + } + support = provenance.get("transcript_read_support") + if support is not None: + evidence["transcript_read_support"] = { + "schema": support["schema"], "file": support["file"], "columns": support["columns"], + "records": [deepcopy(r) for r in support["records"] + if r["transcript_model_id"] == row["exacto_transcript_model_id"]], + } + fragments.append(ProteinFragment( + fragment_id=make_fragment_id("exacto", row["sequence"], qualifiers=[identity]), + sample_name=row["sample_name"], source_type=row["source_type"], sequence=row["sequence"], + target_intervals=None if intervals is None else [tuple(pair) for pair in intervals], + annotations={"exacto": evidence, "exacto_observation": row, + "sequence_source": row["sequence_source"], "tumor_specificity": None}, + )) + return fragments From b4e23f3a0a5951716b602059fc6ebfda1b531ab8 Mon Sep 17 00:00:00 2001 From: Alex Rubinsteyn Date: Tue, 29 Sep 2026 15:16:53 -0400 Subject: [PATCH 2/2] Load Exacto codon tables only during translation validation --- topiary/io_exacto.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/topiary/io_exacto.py b/topiary/io_exacto.py index 1c0f09d..53279b5 100644 --- a/topiary/io_exacto.py +++ b/topiary/io_exacto.py @@ -8,7 +8,6 @@ from pathlib import Path import pandas as pd -from varcode.effects.codon_tables import STANDARD from .candidates import _identity from .protein_fragment import ProteinFragment, make_fragment_id @@ -85,6 +84,8 @@ def _ids(value): def _translated(coding): + from varcode.effects.codon_tables import STANDARD + return "".join("*" if coding[i:i + 3] in STANDARD.stop_codons else STANDARD.forward_table.get(coding[i:i + 3], "X") for i in range(0, len(coding) - 2, 3))