sniffcell-lite 0.9.6__tar.gz

sniffcell_lite-0.9.6/LICENSE

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+MIT License
+
+Copyright (c) 2024 Yilei Fu
+
+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.

sniffcell_lite-0.9.6/PKG-INFO

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+Metadata-Version: 2.4
+Name: sniffcell-lite
+Version: 0.9.6
+Summary: SniffCell Lite annotates variants using targeted long-read methylation evidence and ctDMR signals.
+Home-page: https://github.com/Fu-Yilei/SniffCell
+Author: Yilei Fu
+Author-email: yilei.fu@bcm.edu
+License: MIT
+Project-URL: Bug Tracker, https://github.com/Fu-Yilei/SniffCell/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pysam>=0.21.0
+Requires-Dist: numpy>=2.2.0
+Requires-Dist: pandas>=2.3.0
+Requires-Dist: scipy
+Requires-Dist: tqdm
+Dynamic: license-file
+
+# SniffCell Lite
+
+SniffCell Lite keeps only two commands:
+
+- `sniffcell-lite find`: call ctDMR catalogs from a methylation atlas.
+- `sniffcell-lite anno`: annotate variants from supporting reads, a BAM, a reference FASTA, and a ctDMR catalog.
+
+This branch intentionally keeps only the lite `find` and `anno` workflow.
+
+## Install
+
+```bash
+pip install .
+```
+
+## Find
+
+`find` keeps the original atlas-driven flavor. The bundled tissue atlas supports tissue code or tissue name lookup through `-ck`.
+
+```bash
+sniffcell-lite find \
+  -n atlas/all_celltypes_blocks.npy \
+  -i atlas/all_celltypes_blocks.index.gz \
+  -m atlas/all_celltypes.txt \
+  -ck "Colon, Ascending" \
+  -o colon_ascending.ctdmr.tsv
+```
+
+Equivalent code form:
+
+```bash
+sniffcell-lite find -ck 3E -o colon_ascending.ctdmr.tsv
+```
+
+The default cell-type JSON is the packaged `sniffcell/data/tissue_atlas.json`. You can still pass a custom atlas with `-cf`.
+
+## Anno
+
+Single-variant mode requires a BAM and reference FASTA. SniffCell Lite maps the variant-supporting reads in the BAM, selects ctDMRs from the catalog that overlap those supporting-read alignment spans, computes methylation from the BAM only for those reads at those ctDMRs, and assigns the variant from the targeted read-level methylation calls. ctDMR evidence is not capped to a fixed distance from the variant.
+
+```bash
+sniffcell-lite anno \
+  -i sample.bam \
+  -r ref.fa \
+  --variant-name variant_001 \
+  --variant-location chr1:100000-101000 \
+  --supporting-reads readA,readB,readC \
+  --catalog colon_ascending.ctdmr.tsv \
+  -o anno_out
+```
+
+Batch mode uses a TSV or CSV with these columns:
+
+```text
+variant_name    variant_location    supporting_reads    catalog    bam    reference
+```
+
+Run:
+
+```bash
+sniffcell-lite anno --batch variants.tsv -o anno_out
+```
+
+`supporting_reads` accepts comma, pipe, semicolon, whitespace-delimited text, JSON list text, or `@path/to/read_names.txt`.
+
+If every batch row uses the same reference, pass it once instead of adding a `reference` column:
+
+```bash
+sniffcell-lite anno --batch variants.tsv -r ref.fa -o anno_out
+```
+
+## Outputs
+
+`sniffcell-lite find` writes:
+
+- `*.tsv`: ctDMR catalog
+- `*.tsv.igv.bed`: IGV BED companion
+- `*.tsv.catalog.json`: catalog manifest when tissue metadata was used
+
+`sniffcell-lite anno` writes:
+
+- `variant_assignment.tsv`
+- `variant_assignment_readable.tsv`
+- `variant_assignment_readable_long.tsv`
+- `reads_classification.tsv`
+- `support_read_mappings.tsv`
+- `anno_compact_manifest.json` or `anno_batch_manifest.json`
+
+## Tests
+
+```bash
+pytest -q
+```

sniffcell_lite-0.9.6/README.md

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+# SniffCell Lite
+
+SniffCell Lite keeps only two commands:
+
+- `sniffcell-lite find`: call ctDMR catalogs from a methylation atlas.
+- `sniffcell-lite anno`: annotate variants from supporting reads, a BAM, a reference FASTA, and a ctDMR catalog.
+
+This branch intentionally keeps only the lite `find` and `anno` workflow.
+
+## Install
+
+```bash
+pip install .
+```
+
+## Find
+
+`find` keeps the original atlas-driven flavor. The bundled tissue atlas supports tissue code or tissue name lookup through `-ck`.
+
+```bash
+sniffcell-lite find \
+  -n atlas/all_celltypes_blocks.npy \
+  -i atlas/all_celltypes_blocks.index.gz \
+  -m atlas/all_celltypes.txt \
+  -ck "Colon, Ascending" \
+  -o colon_ascending.ctdmr.tsv
+```
+
+Equivalent code form:
+
+```bash
+sniffcell-lite find -ck 3E -o colon_ascending.ctdmr.tsv
+```
+
+The default cell-type JSON is the packaged `sniffcell/data/tissue_atlas.json`. You can still pass a custom atlas with `-cf`.
+
+## Anno
+
+Single-variant mode requires a BAM and reference FASTA. SniffCell Lite maps the variant-supporting reads in the BAM, selects ctDMRs from the catalog that overlap those supporting-read alignment spans, computes methylation from the BAM only for those reads at those ctDMRs, and assigns the variant from the targeted read-level methylation calls. ctDMR evidence is not capped to a fixed distance from the variant.
+
+```bash
+sniffcell-lite anno \
+  -i sample.bam \
+  -r ref.fa \
+  --variant-name variant_001 \
+  --variant-location chr1:100000-101000 \
+  --supporting-reads readA,readB,readC \
+  --catalog colon_ascending.ctdmr.tsv \
+  -o anno_out
+```
+
+Batch mode uses a TSV or CSV with these columns:
+
+```text
+variant_name    variant_location    supporting_reads    catalog    bam    reference
+```
+
+Run:
+
+```bash
+sniffcell-lite anno --batch variants.tsv -o anno_out
+```
+
+`supporting_reads` accepts comma, pipe, semicolon, whitespace-delimited text, JSON list text, or `@path/to/read_names.txt`.
+
+If every batch row uses the same reference, pass it once instead of adding a `reference` column:
+
+```bash
+sniffcell-lite anno --batch variants.tsv -r ref.fa -o anno_out
+```
+
+## Outputs
+
+`sniffcell-lite find` writes:
+
+- `*.tsv`: ctDMR catalog
+- `*.tsv.igv.bed`: IGV BED companion
+- `*.tsv.catalog.json`: catalog manifest when tissue metadata was used
+
+`sniffcell-lite anno` writes:
+
+- `variant_assignment.tsv`
+- `variant_assignment_readable.tsv`
+- `variant_assignment_readable_long.tsv`
+- `reads_classification.tsv`
+- `support_read_mappings.tsv`
+- `anno_compact_manifest.json` or `anno_batch_manifest.json`
+
+## Tests
+
+```bash
+pytest -q
+```

sniffcell_lite-0.9.6/pyproject.toml

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+[build-system]
+requires = [
+    "setuptools>=64",
+    "wheel"
+]
+build-backend = "setuptools.build_meta"

sniffcell_lite-0.9.6/setup.cfg

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+[metadata]
+name = sniffcell-lite
+version = 0.9.6
+author = Yilei Fu
+author_email = yilei.fu@bcm.edu
+description = SniffCell Lite annotates variants using targeted long-read methylation evidence and ctDMR signals.
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/Fu-Yilei/SniffCell
+license = MIT
+project_urls = 
+	Bug Tracker = https://github.com/Fu-Yilei/SniffCell/issues
+classifiers = 
+	Programming Language :: Python :: 3
+	License :: OSI Approved :: MIT License
+	Operating System :: OS Independent
+
+[options]
+package_dir = 
+	= src
+packages = find:
+python_requires = >=3.10
+install_requires = 
+	pysam>=0.21.0
+	numpy>=2.2.0
+	pandas>=2.3.0
+	scipy
+	tqdm
+include_package_data = True
+
+[options.package_data]
+sniffcell = 
+	data/*.json
+
+[options.packages.find]
+where = src
+
+[options.entry_points]
+console_scripts = 
+	sniffcell-lite = sniffcell.main:main
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

sniffcell_lite-0.9.6/src/sniffcell/__init__.py

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+__version__ = "v0.9.6"