fetchm2 0.1.0__py3-none-any.whl

fetchm2-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: fetchm2
+Version: 0.1.0
+Summary: Standalone comprehensive genome metadata standardization and sequence download toolkit.
+Author-email: Tasnimul Arabi Anik <arabianik987@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/Tasnimul-Arabi-Anik/FetchM2
+Project-URL: Repository, https://github.com/Tasnimul-Arabi-Anik/FetchM2
+Project-URL: Issues, https://github.com/Tasnimul-Arabi-Anik/FetchM2/issues
+Keywords: NCBI,BioSample,metadata,genomics,standardization,sequence-download
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pandas>=2.0
+Requires-Dist: requests>=2.31
+Requires-Dist: tqdm>=4.66
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: seaborn>=0.13
+Requires-Dist: plotly>=5.20
+Requires-Dist: kaleido<1.0.0,>=0.2.1
+Requires-Dist: xmltodict>=0.13
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0; extra == "dev"
+Requires-Dist: build>=1.2; extra == "dev"
+Requires-Dist: twine>=5.0; extra == "dev"
+Dynamic: license-file
+
+# FetchM2
+
+FetchM2 is a standalone command-line toolkit for genome metadata retrieval, comprehensive metadata standardization, audit reporting, and optional sequence download.
+
+It keeps the simple standalone installation model of the original public [`FetchM`](https://github.com/Tasnimul-Arabi-Anik/FetchM), while packaging deterministic rule files and QA concepts developed in FetchM Web.
+
+## What FetchM2 Does
+
+- Reads NCBI Genome Datasets TSV/CSV exports.
+- Optionally fetches linked BioSample metadata from NCBI.
+- Standardizes host, country/geography, collection year, sample type, isolation source, isolation site, environment medium, host disease, and host health state.
+- Adds host TaxID, rank, lineage fields, match method, confidence, and review status.
+- Writes clean metadata tables and audit reports.
+- Downloads genome FASTA files from NCBI with flexible filters.
+- Runs offline on already annotated tables for reproducible tests and local standardization.
+
+## Installation
+
+Recommended clean environment:
+
+```bash
+python -m venv fetchm2-env
+source fetchm2-env/bin/activate
+pip install fetchm2
+```
+
+For development from source:
+
+```bash
+git clone https://github.com/Tasnimul-Arabi-Anik/FetchM2.git
+cd FetchM2
+python -m pip install -e ".[dev]"
+pytest
+```
+
+FetchM2 uses Python dependencies only. `taxonkit` is optional. If available, FetchM2 can use it to enrich less common host TaxIDs with lineage fields; common host lineages are bundled.
+
+## Quick Start
+
+Offline smoke test using the bundled example:
+
+```bash
+fetchm2 metadata --input examples/offline_metadata.tsv --outdir demo_out --offline
+```
+
+Full BioSample metadata retrieval:
+
+```bash
+fetchm2 metadata --input ncbi_dataset.tsv --outdir results
+```
+
+With NCBI API key:
+
+```bash
+export NCBI_API_KEY=YOUR_NCBI_API_KEY
+fetchm2 metadata --input ncbi_dataset.tsv --outdir results --workers 6 --sleep 0.15
+```
+
+All-in-one metadata plus sequence download:
+
+```bash
+fetchm2 run --input ncbi_dataset.tsv --outdir results --download
+```
+
+Filtered sequence download from a clean table:
+
+```bash
+fetchm2 seq \
+  --input results/metadata_output/fetchm2_clean.csv \
+  --outdir results/sequence \
+  --host "Homo sapiens" \
+  --country Bangladesh \
+  --year-from 2018 \
+  --year-to 2024
+```
+
+## Main Commands
+
+```bash
+fetchm2 metadata --help
+fetchm2 run --help
+fetchm2 seq --help
+fetchm2 audit --help
+```
+
+## Metadata Outputs
+
+FetchM2 writes:
+
+- `metadata_output/fetchm2_clean.csv`
+- `metadata_output/fetchm2_clean.tsv`
+- `metadata_output/fetchm2_report.md`
+- `audit/standardization_summary.csv`
+- `audit/top_host_review_needed.csv`
+- `audit/standardization_audit.md`
+
+Important standardized fields include:
+
+- `Host_SD`, `Host_TaxID`, `Host_Rank`, `Host_Superkingdom`, `Host_Phylum`, `Host_Class`, `Host_Order`, `Host_Family`, `Host_Genus`, `Host_Species`
+- `Host_Common_Name`, `Host_Match_Method`, `Host_Confidence`, `Host_Review_Status`
+- `Sample_Type_SD`, `Sample_Type_SD_Broad`
+- `Isolation_Source_SD`, `Isolation_Source_SD_Broad`
+- `Isolation_Site_SD`
+- `Environment_Medium_SD`, `Environment_Medium_SD_Broad`
+- `Environment_Broad_Scale_SD`, `Environment_Local_Scale_SD`
+- `Host_Disease_SD`, `Host_Health_State_SD`
+- `Country`, `Continent`, `Subcontinent`, `Collection_Year`
+
+## Sequence Download Options
+
+FetchM2 supports filtering by:
+
+- host
+- host rank
+- country
+- continent
+- subcontinent
+- sample type
+- isolation source
+- environment medium
+- collection year range
+- maximum genomes
+
+Use `--check-only` to audit a sequence output directory without downloading.
+
+## API Keys
+
+For NCBI, prefer environment variables:
+
+```bash
+export NCBI_API_KEY=YOUR_NCBI_API_KEY
+export NCBI_EMAIL=you@example.com
+```
+
+Do not place API keys in scripts, notebooks, README files, or Git commits.
+
+## Design Compared With FetchM and FetchM Web
+
+FetchM2 uses the original FetchM standalone flow as the command-line baseline:
+
+- metadata
+- run
+- seq
+- SQLite cache
+- NCBI BioSample fetch
+- sequence download from NCBI FTP
+
+FetchM2 adds FetchM Web-style standardized metadata fields and deterministic rule files:
+
+- host synonyms and negative host rules
+- controlled source/sample/environment categories
+- approved broad vocabulary
+- production-style audit gate
+- richer sequence filtering on standardized fields
+
+FetchM2 intentionally does not use embeddings or AI for production mappings. Embeddings can be used later as a review assistant, but final production rules should remain deterministic and auditable.
+
+## Testing
+
+Run:
+
+```bash
+pytest
+python -m build
+python -m pip install dist/fetchm2-*.whl
+fetchm2 metadata --input examples/offline_metadata.tsv --outdir smoke_out --offline
+fetchm2 seq --input smoke_out/metadata_output/fetchm2_clean.csv --outdir smoke_seq --country Bangladesh --check-only
+```
+
+## License
+
+MIT License.

fetchm2-0.1.0.dist-info/RECORD

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+fetchm2/cli.py,sha256=roRAzM1eU-hecHqq3BJlzmKuzLMT3t6nGPxEWtJhAtg,8464
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+fetchm2/sequence.py,sha256=7t7C0PZv_aeEA4E0I3SHLxS8Yjz1t1ob4mKc9E8od1E,7956
+fetchm2/standardization.py,sha256=_AciT1VkYWtkWdAu6RpWhpkre6OMxEExHKMSNPmjMlc,20618
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+fetchm2/data/country_mapping.json,sha256=PYk_PGYM1F_uHxpbUXylZIWoPu4NVjKKqvol8t971xQ,17344
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+fetchm2-0.1.0.dist-info/licenses/LICENSE,sha256=8QW78fG4kk5GSOCzLE_D9SrD2eTlANgRr8vc4baQ-MI,1076
+fetchm2-0.1.0.dist-info/METADATA,sha256=IZd-qZ2psh95S3EaSvk7HuDkJEanbr60ke6I_H-vWe0,6240
+fetchm2-0.1.0.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+fetchm2-0.1.0.dist-info/entry_points.txt,sha256=vvc7-U-NmlkAe3LaZArXHEQcp8eilgQKAS-T1FyInt4,72
+fetchm2-0.1.0.dist-info/top_level.txt,sha256=pIvb4NVf1LumJONqwoqxTxErRiLimYFPnaPtpiSuM9I,8
+fetchm2-0.1.0.dist-info/RECORD,,

fetchm2-0.1.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

fetchm2-0.1.0.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+fetchM2 = fetchm2.cli:main
+fetchm2 = fetchm2.cli:main

fetchm2-0.1.0.dist-info/licenses/LICENSE

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+MIT License
+
+Copyright (c) 2026 Tasnimul Arabi Anik
+
+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.

fetchm2-0.1.0.dist-info/top_level.txt

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+fetchm2