protein-fasta 0.3.0__tar.gz

protein_fasta-0.3.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Witold Wolski
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

protein_fasta-0.3.0/LICENSES/Apache-2.0.txt

@@ -0,0 +1,159 @@
+Apache License
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+https://www.apache.org/licenses/
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+END OF TERMS AND CONDITIONS

protein_fasta-0.3.0/LICENSES/BSD-3-Clause-Biopython.txt

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 1999-2024, The Biopython Contributors
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
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+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
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+3. Neither the name of the copyright holder nor the names of its contributors
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protein_fasta-0.3.0/NOTICE

@@ -0,0 +1,33 @@
+Protein FASTA
+Copyright 2026 Witold Wolski
+
+This product includes modified source-derived behavior from FDR Benchmark,
+Copyright 2026 Functional Genomics Center Zurich, revision
+bbf582e382833cf8bdc439e69edb287842293b02, under the Apache License 2.0.
+
+FDR Benchmark in turn records the following attributions:
+
+- PGATK, https://github.com/bigbio/pgatk, reviewed revision cdedf9057e7e.
+  Its DecoyPYrat reverse/switch and collision workflow informed the decoy
+  generation implementation.
+- FDRBench, https://github.com/Noble-Lab/FDRBench, reviewed revision
+  5deac96dfa0e. Its entrapment-generation behavior informed the entrapment
+  generation implementation.
+
+The original projects and associated publications retain their respective
+copyrights and attribution. See LICENSES/Apache-2.0.txt for the applicable
+third-party license.
+
+The dipeptide instability weight values in
+src/protein_fasta/analytics/peptide_properties.py are taken from Biopython
+1.86, Bio/SeqUtils/ProtParamData.py, Copyright (c) 1999-2024 The Biopython
+Contributors, under the BSD 3-Clause License (two entries changed to the
+values of the R package Peptides). See LICENSES/BSD-3-Clause-Biopython.txt.
+
+The reversed-phase retention coefficients and length-corrected retention
+model in the same file are taken from Pyteomics 4.7.5, pyteomics/achrom.py
+(RCs_zubarev, calculate_RT), under the Apache License 2.0; see
+LICENSES/Apache-2.0.txt. Pyteomics: Goloborodko et al., J Am Soc Mass Spectrom
+2013, 24(2):301-304; Levitsky et al., J Proteome Res 2019, 18(2):709-714. The
+coefficients: Goloborodko et al., Rapid Commun Mass Spectrom 2010,
+24(4):454-462.

protein_fasta-0.3.0/PKG-INFO

@@ -0,0 +1,202 @@
+Metadata-Version: 2.4
+Name: protein-fasta
+Version: 0.3.0
+Summary: Streaming protein records and config-driven Polars FASTA frames.
+Keywords: proteomics,fasta,protein database,uniprot,polars
+Author: Witold Wolski
+Author-email: Witold Wolski <wew@fgcz.ethz.ch>
+License-Expression: MIT
+License-File: LICENSE
+License-File: LICENSES/Apache-2.0.txt
+License-File: LICENSES/BSD-3-Clause-Biopython.txt
+License-File: NOTICE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Typing :: Typed
+Requires-Dist: loguru>=0.7,<1
+Requires-Dist: pydantic>=2.13,<3
+Requires-Dist: cyclopts>=4.20,<5 ; extra == 'cli'
+Requires-Dist: httpx>=0.28,<1 ; extra == 'cli'
+Requires-Dist: loguru>=0.7,<1 ; extra == 'cli'
+Requires-Dist: polars>=1.43.2,<2 ; extra == 'cli'
+Requires-Dist: xlsxwriter>=3.2,<4 ; extra == 'cli'
+Requires-Dist: duckdb>=1.4.2,<2 ; extra == 'duckdb'
+Requires-Dist: polars>=1.43.2,<2 ; extra == 'duckdb'
+Requires-Dist: pyarrow>=22 ; extra == 'duckdb'
+Requires-Dist: polars>=1.43.2,<2 ; extra == 'frame'
+Requires-Dist: httpx>=0.28,<1 ; extra == 'uniprot'
+Requires-Dist: polars>=1.43.2,<2 ; extra == 'uniprot'
+Requires-Python: >=3.13
+Project-URL: Documentation, https://anndata-omics-bridge.github.io/protein-fasta/
+Project-URL: Repository, https://github.com/anndata-omics-bridge/protein-fasta
+Provides-Extra: cli
+Provides-Extra: duckdb
+Provides-Extra: frame
+Provides-Extra: uniprot
+Description-Content-Type: text/markdown
+
+# Protein FASTA
+
+`protein-fasta` provides one shared protein-FASTA boundary with deliberately granular APIs:
+
+- a constant-memory Python iterator returning minimal normalized records; and
+- an optional Polars frame reader that enriches homogeneous UniProtKB or RefSeq files from
+  Pydantic-validated JSON rules;
+- backend-free hashing, digestion, comparison, and clustering analytics;
+- reproducible source preparation, biological construction, and subsequent decoy generation;
+- canonical peptide construction and comparison with memory, SQLite, or DuckDB execution;
+- reproducible UniProt proteome catalogs and FASTA acquisition;
+- SQLite or optional DuckDB indexing with materialized pair metrics; and
+- a short, single-word Cyclopts command surface for each reproducible operation.
+
+**[Online documentation](https://anndata-omics-bridge.github.io/protein-fasta/)**
+
+The stable high-level Python record is exactly `id`, optional `description`, and normalized
+`sequence`:
+
+```python
+from pathlib import Path
+
+from protein_fasta.record import iter_proteins
+
+for protein in iter_proteins(Path("proteins.fasta.gz")):
+    print(protein.id, protein.sequence)
+```
+
+Normalization removes FASTA formatting whitespace, upper-cases the sequence, and removes exactly
+one terminal `*`. Callers needing source text use the separately named lower-level
+`read_records()` or header-only `read_headers()` operations; raw headers are never reconstructed
+from normalized fields.
+
+## Configured diagnostics
+
+`ProteinDiagnostics` composes one `ProteinRecord` with the raw header, identifier namespace,
+independent classification labels, normalization changes, and illegal residues:
+
+```python
+from pathlib import Path
+
+from protein_fasta.compile import make_diagnostic_rules
+from protein_fasta.documents import (
+    load_builtin_diagnostic_document,
+    load_builtin_entry_classifier_document,
+)
+from protein_fasta.record import iter_protein_diagnostics
+
+rules = make_diagnostic_rules(
+    load_builtin_diagnostic_document(),
+    load_builtin_entry_classifier_document(),
+)
+diagnostics = iter_protein_diagnostics(Path("proteins.fasta"), rules)
+```
+
+Classifications overlap: a decoy contaminant can report both labels. Configured decorations are
+peeled only from a temporary identifier used for diagnostics and database parsing; the public
+record ID remains unchanged. The packaged classifier document contains only format-independent
+decorations; application-specific marker conventions belong in an explicit classifier document
+supplied to the configured APIs.
+
+For a database-level report, stream those records into the aggregate API:
+
+```python
+from protein_fasta.diagnostic_summary import summarize_protein_diagnostics
+
+summary = summarize_protein_diagnostics(diagnostics)
+print(summary.namespace_counts, summary.classification_counts)
+```
+
+## Polars frames
+
+Install `protein-fasta[frame]`. Applications that need one configured database frame select the
+accepted public formats when constructing `ProteinDatabase`, then supply the ordered FASTA paths to
+`parse()`:
+
+```python
+from pathlib import Path
+
+from protein_fasta.api import ProteinDatabase, refseq, uniprotkb
+
+protein_database = ProteinDatabase(uniprotkb, refseq)
+proteins = protein_database.parse(
+    (Path("human.fasta"), Path("contaminants.fasta")),
+)
+```
+
+The result is one row-wise enriched Polars frame. It includes `id`, `description`, `sequence`, the
+columns selected by the format profiles, classifier columns, and stable path/checksum/source/record
+provenance. Document loading and parser compilation remain private to `protein_fasta`.
+
+Lower-level callers may choose the exact base table or automatic row-wise enrichment:
+
+```python
+from pathlib import Path
+
+from protein_fasta.frame import read_basic_protein_frame, read_protein_frame
+
+base = read_basic_protein_frame(Path("mixed.fasta"))
+best = read_protein_frame(Path("uniprot.fasta"))
+```
+
+`read_basic_protein_frame()` always returns exactly `id`, `description`, and `sequence`.
+`read_protein_frame()` applies the sole matching built-in parser to each row. Unmatched or ambiguous
+rows retain their base values and receive null parser fields. `read_strict_protein_frame()` requires
+one format to match every row and otherwise returns the exact base schema. Built-in database rules
+live in one JSON document per database.
+
+## Table-export CLI
+
+Install the CLI extra and select CSV, TSV, XLSX, or Parquet through the output suffix:
+
+```bash
+pip install 'protein-fasta[cli]'
+protein-fasta table database.fasta proteins.xlsx --no-sequence
+protein-fasta table database.fasta proteins-with-hashes.csv --checksums
+protein-fasta table database.fasta proteins.csv --strict
+protein-fasta basic database.fasta proteins.csv
+protein-fasta formats database.fasta formats.csv
+protein-fasta diagnostics database.fasta
+protein-fasta digest database.fasta peptides.parquet
+protein-fasta checksum database.fasta
+protein-fasta uniprot-download UP000000589 opg
+protein-fasta prepare human.fasta protein-input.parquet --id human-uniprot
+protein-fasta build protein-input.parquet \
+  --output build --project 42261 --dbn 1 --description human
+protein-fasta decoy biological.fasta.protein-inventory.parquet \
+  --output search.fasta --method reverse
+protein-fasta peptides search-inventory.parquet --output peptide-products
+protein-fasta prepare --request protein-input.parquet.request.json \
+  --output replayed-protein-input.parquet
+protein-fasta index databases registry.sqlite3
+protein-fasta index-inventory search-inventory.parquet registry.duckdb --config registry.json
+protein-fasta registry registry.sqlite3 databases.csv
+protein-fasta compare registry.sqlite3 12 comparison.csv
+protein-fasta pairs registry.sqlite3 pairs.tsv
+protein-fasta cluster registry.sqlite3 clustering.csv
+```
+
+Direct workflow commands write their validated authored `*.request.json` before computation.
+Replay one explicitly with `--request`; authored requests, resolved `*.effective.json`, observed
+`*.result.json`, and data artifacts remain separate.
+
+The CLI also exposes aggregate diagnostics, theoretical digestion, checksums, database builds,
+registry indexing, database comparisons, materialized pair exports, and clustering. See the
+[build workflows](https://anndata-omics-bridge.github.io/protein-fasta/workflows/),
+[CLI guide and executable walkthrough](https://anndata-omics-bridge.github.io/protein-fasta/cli_walkthrough/),
+[API reference](https://anndata-omics-bridge.github.io/protein-fasta/api/), and maintained
+[architecture](https://anndata-omics-bridge.github.io/protein-fasta/architecture/).
+
+The package excludes site-specific curated contaminant/QC catalogs, GUI installation workflows,
+protein inference, and AnnData/MuData persistence. Those consumers compose the typed artifacts and
+APIs without owning FASTA, decoy, peptide, UniProt, or registry computation.
+
+## Development
+
+```bash
+uv sync --group dev --extra cli --extra frame --extra duckdb
+make check
+make docs
+```

protein_fasta-0.3.0/README.md

@@ -0,0 +1,161 @@
+# Protein FASTA
+
+`protein-fasta` provides one shared protein-FASTA boundary with deliberately granular APIs:
+
+- a constant-memory Python iterator returning minimal normalized records; and
+- an optional Polars frame reader that enriches homogeneous UniProtKB or RefSeq files from
+  Pydantic-validated JSON rules;
+- backend-free hashing, digestion, comparison, and clustering analytics;
+- reproducible source preparation, biological construction, and subsequent decoy generation;
+- canonical peptide construction and comparison with memory, SQLite, or DuckDB execution;
+- reproducible UniProt proteome catalogs and FASTA acquisition;
+- SQLite or optional DuckDB indexing with materialized pair metrics; and
+- a short, single-word Cyclopts command surface for each reproducible operation.
+
+**[Online documentation](https://anndata-omics-bridge.github.io/protein-fasta/)**
+
+The stable high-level Python record is exactly `id`, optional `description`, and normalized
+`sequence`:
+
+```python
+from pathlib import Path
+
+from protein_fasta.record import iter_proteins
+
+for protein in iter_proteins(Path("proteins.fasta.gz")):
+    print(protein.id, protein.sequence)
+```
+
+Normalization removes FASTA formatting whitespace, upper-cases the sequence, and removes exactly
+one terminal `*`. Callers needing source text use the separately named lower-level
+`read_records()` or header-only `read_headers()` operations; raw headers are never reconstructed
+from normalized fields.
+
+## Configured diagnostics
+
+`ProteinDiagnostics` composes one `ProteinRecord` with the raw header, identifier namespace,
+independent classification labels, normalization changes, and illegal residues:
+
+```python
+from pathlib import Path
+
+from protein_fasta.compile import make_diagnostic_rules
+from protein_fasta.documents import (
+    load_builtin_diagnostic_document,
+    load_builtin_entry_classifier_document,
+)
+from protein_fasta.record import iter_protein_diagnostics
+
+rules = make_diagnostic_rules(
+    load_builtin_diagnostic_document(),
+    load_builtin_entry_classifier_document(),
+)
+diagnostics = iter_protein_diagnostics(Path("proteins.fasta"), rules)
+```
+
+Classifications overlap: a decoy contaminant can report both labels. Configured decorations are
+peeled only from a temporary identifier used for diagnostics and database parsing; the public
+record ID remains unchanged. The packaged classifier document contains only format-independent
+decorations; application-specific marker conventions belong in an explicit classifier document
+supplied to the configured APIs.
+
+For a database-level report, stream those records into the aggregate API:
+
+```python
+from protein_fasta.diagnostic_summary import summarize_protein_diagnostics
+
+summary = summarize_protein_diagnostics(diagnostics)
+print(summary.namespace_counts, summary.classification_counts)
+```
+
+## Polars frames
+
+Install `protein-fasta[frame]`. Applications that need one configured database frame select the
+accepted public formats when constructing `ProteinDatabase`, then supply the ordered FASTA paths to
+`parse()`:
+
+```python
+from pathlib import Path
+
+from protein_fasta.api import ProteinDatabase, refseq, uniprotkb
+
+protein_database = ProteinDatabase(uniprotkb, refseq)
+proteins = protein_database.parse(
+    (Path("human.fasta"), Path("contaminants.fasta")),
+)
+```
+
+The result is one row-wise enriched Polars frame. It includes `id`, `description`, `sequence`, the
+columns selected by the format profiles, classifier columns, and stable path/checksum/source/record
+provenance. Document loading and parser compilation remain private to `protein_fasta`.
+
+Lower-level callers may choose the exact base table or automatic row-wise enrichment:
+
+```python
+from pathlib import Path
+
+from protein_fasta.frame import read_basic_protein_frame, read_protein_frame
+
+base = read_basic_protein_frame(Path("mixed.fasta"))
+best = read_protein_frame(Path("uniprot.fasta"))
+```
+
+`read_basic_protein_frame()` always returns exactly `id`, `description`, and `sequence`.
+`read_protein_frame()` applies the sole matching built-in parser to each row. Unmatched or ambiguous
+rows retain their base values and receive null parser fields. `read_strict_protein_frame()` requires
+one format to match every row and otherwise returns the exact base schema. Built-in database rules
+live in one JSON document per database.
+
+## Table-export CLI
+
+Install the CLI extra and select CSV, TSV, XLSX, or Parquet through the output suffix:
+
+```bash
+pip install 'protein-fasta[cli]'
+protein-fasta table database.fasta proteins.xlsx --no-sequence
+protein-fasta table database.fasta proteins-with-hashes.csv --checksums
+protein-fasta table database.fasta proteins.csv --strict
+protein-fasta basic database.fasta proteins.csv
+protein-fasta formats database.fasta formats.csv
+protein-fasta diagnostics database.fasta
+protein-fasta digest database.fasta peptides.parquet
+protein-fasta checksum database.fasta
+protein-fasta uniprot-download UP000000589 opg
+protein-fasta prepare human.fasta protein-input.parquet --id human-uniprot
+protein-fasta build protein-input.parquet \
+  --output build --project 42261 --dbn 1 --description human
+protein-fasta decoy biological.fasta.protein-inventory.parquet \
+  --output search.fasta --method reverse
+protein-fasta peptides search-inventory.parquet --output peptide-products
+protein-fasta prepare --request protein-input.parquet.request.json \
+  --output replayed-protein-input.parquet
+protein-fasta index databases registry.sqlite3
+protein-fasta index-inventory search-inventory.parquet registry.duckdb --config registry.json
+protein-fasta registry registry.sqlite3 databases.csv
+protein-fasta compare registry.sqlite3 12 comparison.csv
+protein-fasta pairs registry.sqlite3 pairs.tsv
+protein-fasta cluster registry.sqlite3 clustering.csv
+```
+
+Direct workflow commands write their validated authored `*.request.json` before computation.
+Replay one explicitly with `--request`; authored requests, resolved `*.effective.json`, observed
+`*.result.json`, and data artifacts remain separate.
+
+The CLI also exposes aggregate diagnostics, theoretical digestion, checksums, database builds,
+registry indexing, database comparisons, materialized pair exports, and clustering. See the
+[build workflows](https://anndata-omics-bridge.github.io/protein-fasta/workflows/),
+[CLI guide and executable walkthrough](https://anndata-omics-bridge.github.io/protein-fasta/cli_walkthrough/),
+[API reference](https://anndata-omics-bridge.github.io/protein-fasta/api/), and maintained
+[architecture](https://anndata-omics-bridge.github.io/protein-fasta/architecture/).
+
+The package excludes site-specific curated contaminant/QC catalogs, GUI installation workflows,
+protein inference, and AnnData/MuData persistence. Those consumers compose the typed artifacts and
+APIs without owning FASTA, decoy, peptide, UniProt, or registry computation.
+
+## Development
+
+```bash
+uv sync --group dev --extra cli --extra frame --extra duckdb
+make check
+make docs
+```