pyvariantdb 1.1__tar.gz

pyvariantdb-1.1/MANIFEST.in

@@ -0,0 +1 @@
+recursive-include pyvariantdb/assets *

pyvariantdb-1.1/PKG-INFO

@@ -0,0 +1,93 @@
+Metadata-Version: 2.4
+Name: pyvariantdb
+Version: 1.1
+Summary: A python package to download, process and access dbSNP data.
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: twine; extra == "test"
+Requires-Dist: pre-commit; extra == "test"
+Requires-Dist: pytest-ruff; extra == "test"
+Requires-Dist: ruff; extra == "test"
+Provides-Extra: prod
+Requires-Dist: pyvariantdb; extra == "prod"
+Provides-Extra: all
+Requires-Dist: pyvariantdb[test]; extra == "all"
+
+# dbSNP to Parquet Converter
+
+A python-package focused rewrite of [Weinstock's dbSNP](https://github.com/weinstockj/dbSNP_to_parquet) to parquet
+repository.
+This package allows convenient download, processing and access to data from dbSNP. A simple python interface
+can be used to work with the data once it is processed.
+
+## Installation
+
+`pyvariantdb` is available on PyPI and can be installed from there with the package management tool of choice. For
+development we use pixi:
+
+```bash
+# install pixi
+curl -fsSL https://pixi.sh/install.sh | sh
+pixi update && pixi install
+```
+
+## Usage
+
+We recommend to prepare the data from the command line before using the package since download and processing takes
+quit some time. Per default the data is stored at ~/.cache/pyvariantdb. This can be changed through the usage of
+environment variables:
+
+```bash
+export PYVARIANTDB_HOME = "/raid/cache/pyvariantdb"
+```
+
+Execution of the pipeline can be done with:
+
+```bash
+# activate pixi
+pixi shell -e default
+# download dbsnp
+pyvariantdb-download
+# transform the database to parquets
+pyvariantdb-make-dbsnp 
+```
+
+We aim to provide an easy interface to extract genomic coordinates from dbSNP. For this, the main functionality
+is extremely simple. Just provide the rs-identifier (with or without chromosome) and we fetch the respective
+coordindates. However, to achieve this we need to run the pipeline mentioned above.
+
+Extracting coordinates is simple:
+
+```python
+from pyvariantdb.lookup import SNPLookup
+
+lookup = SNPLookup()
+# P53 mutations, chromosome 17
+rsids = ["rs1042522", "rs17878362", "rs1800372"]
+df_all = lookup.query_all(rsids)
+df_chr = lookup.query_chromosome(rsids, "17")
+print(df_all)
+print(df_chr) 
+```
+
+## Processing Pipeline
+
+`pyvariantdb` offers some quality of life improvements for working with dbSNP and the original repository.
+The original pipeline remains the same:
+
+1. Downloads dbSNP data (GRCh38 build 156)
+2. Filters for SNVs only
+3. Converts chromosome contigs to standard naming
+4. Splits data by chromosome
+5. Creates Parquet lookup tables with RSID mappings
+
+## Output
+
+The script entrypoint generates the following files on-disk to the defined cache dir.
+
+- `dbSNP_156.bcf` - Full filtered BCF file
+- `dbSNP_156.chr*.bcf` - Per-chromosome BCF files
+- `dbSNP_156.chr*.lookup.parquet` - Per-chromosome RSID lookup tables
+- `dbSNP_156.lookup.parquet` - Combined RSID lookup table

pyvariantdb-1.1/README.md

@@ -0,0 +1,76 @@
+# dbSNP to Parquet Converter
+
+A python-package focused rewrite of [Weinstock's dbSNP](https://github.com/weinstockj/dbSNP_to_parquet) to parquet
+repository.
+This package allows convenient download, processing and access to data from dbSNP. A simple python interface
+can be used to work with the data once it is processed.
+
+## Installation
+
+`pyvariantdb` is available on PyPI and can be installed from there with the package management tool of choice. For
+development we use pixi:
+
+```bash
+# install pixi
+curl -fsSL https://pixi.sh/install.sh | sh
+pixi update && pixi install
+```
+
+## Usage
+
+We recommend to prepare the data from the command line before using the package since download and processing takes
+quit some time. Per default the data is stored at ~/.cache/pyvariantdb. This can be changed through the usage of
+environment variables:
+
+```bash
+export PYVARIANTDB_HOME = "/raid/cache/pyvariantdb"
+```
+
+Execution of the pipeline can be done with:
+
+```bash
+# activate pixi
+pixi shell -e default
+# download dbsnp
+pyvariantdb-download
+# transform the database to parquets
+pyvariantdb-make-dbsnp 
+```
+
+We aim to provide an easy interface to extract genomic coordinates from dbSNP. For this, the main functionality
+is extremely simple. Just provide the rs-identifier (with or without chromosome) and we fetch the respective
+coordindates. However, to achieve this we need to run the pipeline mentioned above.
+
+Extracting coordinates is simple:
+
+```python
+from pyvariantdb.lookup import SNPLookup
+
+lookup = SNPLookup()
+# P53 mutations, chromosome 17
+rsids = ["rs1042522", "rs17878362", "rs1800372"]
+df_all = lookup.query_all(rsids)
+df_chr = lookup.query_chromosome(rsids, "17")
+print(df_all)
+print(df_chr) 
+```
+
+## Processing Pipeline
+
+`pyvariantdb` offers some quality of life improvements for working with dbSNP and the original repository.
+The original pipeline remains the same:
+
+1. Downloads dbSNP data (GRCh38 build 156)
+2. Filters for SNVs only
+3. Converts chromosome contigs to standard naming
+4. Splits data by chromosome
+5. Creates Parquet lookup tables with RSID mappings
+
+## Output
+
+The script entrypoint generates the following files on-disk to the defined cache dir.
+
+- `dbSNP_156.bcf` - Full filtered BCF file
+- `dbSNP_156.chr*.bcf` - Per-chromosome BCF files
+- `dbSNP_156.chr*.lookup.parquet` - Per-chromosome RSID lookup tables
+- `dbSNP_156.lookup.parquet` - Combined RSID lookup table

pyvariantdb-1.1/pyproject.toml

@@ -0,0 +1,54 @@
+[project]
+name = "pyvariantdb"
+version = "1.1"
+description = "A python package to download, process and access dbSNP data."
+readme = "README.md"
+requires-python = ">=3.11"
+
+[project.scripts]
+pyvariantdb-download = "pyvariantdb.download:download_dbsnp"
+pyvariantdb-snp2parquet = "pyvariantdb.scripts.convert:main"
+pyvariantdb-make-dbsnp = "pyvariantdb.scripts.dbsnp2parquet:main"
+
+# ---- build
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+include = ["pyvariantdb"]
+
+# -- pixi settings
+[tool.pixi.workspace]
+channels = ["conda-forge", "bioconda"]
+platforms = ["linux-64", "osx-arm64"]
+
+
+[tool.pixi.dependencies]
+python = "*"
+bcftools = "*"
+pandas = "*"
+polars = "*"
+cyvcf2 = "*"
+snakemake-executor-plugin-cluster-generic = "*"
+snakemake = "*"
+pyarrow = "*"
+ipython = "*"
+loguru = "*"
+aria2 = "*"
+
+[tool.pixi.pypi-dependencies]
+pyvariantdb = { path = ".", editable = true}
+
+[project.optional-dependencies]
+test = ["pytest", "twine", "pre-commit", "pytest-ruff", "ruff"]
+prod = ["pyvariantdb"]
+all = ["pyvariantdb[test]"]
+
+[tool.pixi.environments]
+default = { features = ["all"], solve-group = "default" }
+prod = { features = ["prod"], solve-group = "default" }
+test = { features = ["test"], solve-group = "default" }
+
+[tool.pixi.feature.test.tasks]
+download = "pytest"

pyvariantdb-1.1/pyvariantdb/__init__.py

@@ -0,0 +1,7 @@
+"""pyvariantdb - A python package to download, process and access dbSNP data."""
+
+import importlib
+
+__all__ = ["__version__"]
+
+__version__ = importlib.metadata.version(__name__)

pyvariantdb-1.1/pyvariantdb/assets/Snakefile

@@ -0,0 +1,129 @@
+"""Snakemake workflow for processing of dbSNP.
+
+This workflow downloads, processes, and converts dbSNP data (GRCh38 build 156) to Parquet format.
+
+Pipeline Steps:
+    1. convert_contig: Downloads and filters dbSNP data for SNVs only
+    2. subset_BCF: Splits data by chromosome
+    3. convert_parquet: Converts each chromosome to Parquet lookup tables
+    4. combine_all_parquets: Combines all chromosome-specific parquet files into one
+
+Usage Examples:
+    # Run all rules (default)
+    >>> snakemake --cores all
+
+    # Run on a cluster with SLURM
+    >>> snakemake --cluster "sbatch -p {resources.partition} --mem={resources.mem} -t {resources.time} -c {threads}" -j 23
+
+    # Run only the combine_all_parquets rule
+    >>> snakemake --cores 1 output/dbSNP_156.combined.lookup.parquet
+
+    # Use a custom config file
+    >>> snakemake --configfile my_config.yaml --cores all
+
+    # Dry run to see what will be executed
+    >>> snakemake -n
+
+"""
+import yaml
+from importlib.resources import files
+from loguru import logger
+
+from pyvariantdb.const import get_cache_dir
+
+pyvariant_assets_dir = files("pyvariantdb") / "assets"
+pyvariant_contigs = pyvariant_assets_dir / "contig_map.tsv"
+pyvariant_config = pyvariant_assets_dir / "config.yaml"
+
+# Use packaged config only when no config was provided on the command line.
+if not config:
+    with open(pyvariant_config,"r") as f:
+        config = yaml.safe_load(f)
+
+CHROMS = [f"chr{x}" for x in range(1,23)] + ['chrX']
+
+config["output_dir"] = get_cache_dir()
+
+logger.info("Starting snakemake workflow from pyvariantdb to download variants.")
+for conf_key, conf_value in config.items():
+    logger.info(f"{conf_key}: {conf_value}")
+
+rule all:
+    input:
+        f"{config['output_dir']}/dbSNP_156.bcf",
+        expand(f"{config['output_dir']}/dbSNP_156.{{CHROM}}.bcf",CHROM=CHROMS),
+        expand(f"{config['output_dir']}/dbSNP_156.{{CHROM}}.lookup.parquet",CHROM=CHROMS),
+        f"{config['output_dir']}/dbSNP_156.combined.lookup.parquet"
+
+rule convert_contig:
+    input:
+        f"{config['output_dir']}/GCF_000001405.40.gz"
+    output:
+        f"{config['output_dir']}/dbSNP_156.bcf"
+    threads: config['resources']['convert_contig']['threads']
+    resources:
+        mem=config['resources']['convert_contig']['mem'],
+        partition=config['cluster']['partition'],
+        time=config['resources']['convert_contig']['time']
+    shell:
+        """
+        bcftools view -i "INFO/VC='SNV'" {input} | 
+            bcftools annotate --rename-chrs {pyvariant_contigs} -Ob --threads {threads} > {output}
+
+        bcftools index {output}
+        """
+
+rule subset_BCF:
+    input:
+        f"{config['output_dir']}/dbSNP_156.bcf"
+    output:
+        f"{config['output_dir']}/dbSNP_156.{{CHROM}}.bcf"
+    threads: config['resources']['subset_BCF']['threads']
+    resources:
+        mem=config['resources']['subset_BCF']['mem'],
+        partition=config['cluster']['partition'],
+        time=config['resources']['subset_BCF']['time']
+    shell:
+        """
+        bcftools view -Ob --threads {threads} {input} {wildcards.CHROM} > {output}
+        bcftools index {output}
+        """
+
+rule convert_parquet:
+    input:
+        f"{config['output_dir']}/dbSNP_156.{{CHROM}}.bcf"
+    output:
+        f"{config['output_dir']}/dbSNP_156.{{CHROM}}.lookup.parquet"
+    resources:
+        mem=config['resources']['convert_parquet']['mem'],
+        partition=config['cluster']['partition'],
+        time=config['resources']['convert_parquet']['time']
+    shell:
+        """
+        pyvariantdb-snp2parquet {input} {output}
+        """
+
+rule combine_all_parquets:
+    input:
+        expand(f"{config['output_dir']}/dbSNP_156.{{CHROM}}.lookup.parquet",CHROM=CHROMS)
+    output:
+        f"{config['output_dir']}/dbSNP_156.combined.lookup.parquet"
+    resources:
+        mem=config['resources'].get('combine_all_parquets',{}).get('mem','16G'),
+        partition=config['cluster']['partition'],
+        time=config['resources'].get('combine_all_parquets',{}).get('time','02:00:00')
+    run:
+        import pyarrow.parquet as pq
+        import pyarrow as pa
+
+        # Read all parquet files
+        tables = []
+        for input_file in input:
+            table = pq.read_table(input_file)
+            tables.append(table)
+
+        # Concatenate all tables
+        combined_table = pa.concat_tables(tables)
+
+        # Write the combined table
+        pq.write_table(combined_table,output[0])

pyvariantdb-1.1/pyvariantdb/assets/config.yaml

@@ -0,0 +1,20 @@
+output_dir: "output"
+
+cluster:
+  partition: "nodes*"
+  
+resources:
+  convert_contig:
+    mem: "6G"
+    time: "07:30:00"
+    threads: 10
+  subset_BCF:
+    mem: "3G"
+    time: "03:30:00"  
+    threads: 10
+  convert_parquet:
+    mem: "8G"
+    time: "05:30:00"
+  combine_all_parquets:
+    mem: "16G"
+    time: "02:00:00"

pyvariantdb-1.1/pyvariantdb/assets/contig_map.tsv

@@ -0,0 +1,24 @@
+NC_000001.11 chr1
+NC_000002.12 chr2
+NC_000003.12 chr3
+NC_000004.12 chr4
+NC_000005.10 chr5
+NC_000006.12 chr6
+NC_000007.14 chr7
+NC_000008.11 chr8
+NC_000009.12 chr9
+NC_000010.11 chr10
+NC_000011.10 chr11
+NC_000012.12 chr12
+NC_000013.11 chr13
+NC_000014.9 chr14
+NC_000015.10 chr15
+NC_000016.10 chr16
+NC_000017.11 chr17
+NC_000018.10 chr18
+NC_000019.10 chr19
+NC_000020.11 chr20
+NC_000021.9 chr21
+NC_000022.11 chr22
+NC_000023.11 chrX
+NC_000024.10 chrY

pyvariantdb-1.1/pyvariantdb/const.py

@@ -0,0 +1,14 @@
+"""Define constants used in pyvariantdb."""
+
+import os
+from loguru import logger
+from pathlib import Path
+
+
+def get_cache_dir() -> None:
+    """Return the root directory of the project."""
+    # check if env var PYVARIANTDB_HOME exists, otherwise ~/.cache/pyvariantdb
+    cache_dir = os.getenv("PYVARIANTDB_HOME", Path().home() / ".cache" / "pyvariantdb")
+    cache_dir.mkdir(parents=True, exist_ok=True)
+    logger.info(f"Cache directory: {cache_dir}")
+    return cache_dir

pyvariantdb-1.1/pyvariantdb/download.py

@@ -0,0 +1,96 @@
+#!/usr/bin/env python3
+"""Download utilities for dbSNP to Parquet conversion."""
+
+import subprocess
+from pathlib import Path
+from loguru import logger
+from pyvariantdb.const import get_cache_dir
+
+
+def download_with_aria2(url: str, output_dir: Path, filename: str = None):
+    """
+    Download a file using aria2c.
+
+    Args:
+        url: The URL to download from
+        output_dir: Directory where the file should be saved
+        filename: Optional custom filename (defaults to name from URL)
+
+    Returns:
+        Path: Path to the downloaded file
+
+    Raises:
+        RuntimeError: If aria2c is not installed or download fails
+    """
+    # Ensure output directory exists
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    # Build aria2c command
+    cmd = [
+        "aria2c",
+        "--dir",
+        str(output_dir),
+        "--max-connection-per-server=16",  # Use up to 16 connections per server
+        "--split=16",  # Split file into 16 pieces for parallel download
+        "--min-split-size=1M",  # Minimum size for splitting
+        "--continue=true",  # Continue partial downloads
+        "--allow-overwrite=true",  # Allow overwriting existing files
+        "--auto-file-renaming=false",  # Don't auto-rename files
+    ]
+
+    if filename:
+        cmd.extend(["--out", filename])
+
+    cmd.append(url)
+
+    # Run aria2c
+    logger.info(f"Running: {' '.join(cmd)}")
+    result = subprocess.run(cmd, capture_output=True, text=True)
+
+    if result.returncode != 0:
+        logger.error(f"aria2c stderr: {result.stderr}")
+        raise RuntimeError(f"Failed to download {url}: {result.stderr}")
+
+    # Determine output path
+    if filename:
+        output_path = output_dir / filename
+    else:
+        output_path = output_dir / url.split("/")[-1]
+
+    return output_path
+
+
+def download_dbsnp():
+    """
+    Download dbSNP VCF file and its index from NCBI's FTP server using aria2.
+
+    Downloads:
+    - GCF_000001405.40.gz (main VCF file)
+    - GCF_000001405.40.gz.tbi (index file)
+
+    Uses aria2c for fast multi-connection downloads.
+    """
+    logger.info("Starting dbSNP download with aria2...")
+
+    urls = [
+        "https://ftp.ncbi.nih.gov/snp/latest_release/VCF/GCF_000001405.40.gz",
+        "https://ftp.ncbi.nih.gov/snp/latest_release/VCF/GCF_000001405.40.gz.tbi",
+    ]
+    destination_dir = get_cache_dir()
+    logger.info(f"Destination directory: {destination_dir}")
+
+    for url in urls:
+        try:
+            filename = url.split("/")[-1]
+            logger.info(f"Downloading {url}...")
+            output_path = download_with_aria2(url, destination_dir, filename)
+            logger.info(f"✓ Successfully downloaded to {output_path}")
+        except Exception as e:
+            logger.error(f"Failed to download {url}: {e}")
+            raise
+
+    logger.info("Download completed successfully!")
+
+
+if __name__ == "__main__":
+    download_dbsnp()

pyvariantdb-1.1/pyvariantdb/lookup.py

@@ -0,0 +1,110 @@
+"""Lookup utilities for dbSNP Parquet outputs.
+
+This module provides lightweight query helpers over per-chromosome dbSNP
+lookup Parquet files generated by the pipeline.
+
+In ideal cases, you already know which chromsome holds a specific rsID. In this case,
+its most efficient to just query the respective chromosome file.
+
+Example:
+    from pyvariantdb.lookup import SNPLookup
+
+    lookup = SNPLookup()
+    # P53 mutations, chromosome 17
+    rsids = ["rs1042522", "rs17878362", "rs1800372"]
+    df_all = lookup.query_all(rsids)
+    df_chr = lookup.query_chromosome(rsids, "17")
+    print(df_all)
+    print(df_chr)
+"""
+
+from __future__ import annotations
+
+import polars as pl
+from loguru import logger
+from pathlib import Path
+from typing import Optional
+
+from pyvariantdb.const import get_cache_dir
+
+DEFAULT_VERSION = "156"
+DEFAULT_OUTPUT_DIR = "output"
+
+
+class SNPLookup:
+    """Query dbSNP lookup Parquet files by rsID.
+
+    Example:
+        lookup = SNPLookup(version="156")
+        rsids = ["rs1042522", "rs17878362", "rs1800372"]
+        df = lookup.query_all(rsids)
+        print(df)
+    """
+
+    def __init__(self, version: str = DEFAULT_VERSION, cache_dir: Optional[str] = None):
+        self.version = version
+        self.cache_dir = (
+            Path(cache_dir) if cache_dir else get_cache_dir() / DEFAULT_OUTPUT_DIR
+        )
+
+    def query_all(self, rsids: list[str]) -> pl.DataFrame:
+        """Query all lookup files for a list of rsIDs.
+
+        Args:
+            rsids: List of rsIDs to search for.
+
+        Returns:
+            A Polars DataFrame with columns "RSID" and "ID".
+
+        Example:
+            lookup = SNPLookup()
+            rsids = ["rs1042522", "rs17878362", "rs1800372"]
+            df = lookup.query_all(rsids)
+            print(df.head(3))
+        """
+        logger.info(f"Querying dbSNP Parquet files for {len(rsids)} rsIDs...")
+        if not rsids:
+            return pl.DataFrame(schema={"RSID": pl.String, "ID": pl.String})
+
+        pattern = f"dbSNP_{self.version}.chr*.lookup.parquet"
+        lookup_files = sorted(self.cache_dir.glob(pattern))
+        if not lookup_files:
+            raise FileNotFoundError(f"No dbSNP Parquet files found in {self.cache_dir}")
+
+        lazy_frames = []
+        for in_file in lookup_files:
+            lazy_frames.append(
+                pl.scan_parquet(in_file).filter(pl.col("RSID").is_in(rsids))
+            )
+
+        return pl.concat(lazy_frames).collect()
+
+    def query_chromosome(self, rsids: list[str], chrom: str) -> pl.DataFrame:
+        """Query a specific chromosome lookup file for a list of rsIDs.
+
+        Args:
+            rsids: List of rsIDs to search for.
+            chrom: Chromosome label, e.g. "chr17" or "17".
+
+        Returns:
+            A Polars DataFrame with columns "RSID" and "ID".
+
+        Example:
+            lookup = SNPLookup()
+            rsids = ["rs1042522", "rs17878362", "rs1800372"]
+            df = lookup.query_chromosome(rsids, "17")
+            print(df)
+        """
+        logger.info(f"Querying dbSNP Parquet files for {len(rsids)} rsIDs...")
+        if not rsids:
+            return pl.DataFrame(schema={"RSID": pl.String, "ID": pl.String})
+
+        chrom_label = chrom if chrom.startswith("chr") else f"chr{chrom}"
+        in_file = self.cache_dir / f"dbSNP_{self.version}.{chrom_label}.lookup.parquet"
+        if not in_file.exists():
+            raise FileNotFoundError(f"dbSNP Parquet file not found: {in_file}")
+
+        subset_df = (
+            pl.scan_parquet(in_file).filter(pl.col("RSID").is_in(rsids)).collect()
+        )
+        return subset_df

pyvariantdb-1.1/pyvariantdb.egg-info/PKG-INFO

@@ -0,0 +1,93 @@
+Metadata-Version: 2.4
+Name: pyvariantdb
+Version: 1.1
+Summary: A python package to download, process and access dbSNP data.
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: twine; extra == "test"
+Requires-Dist: pre-commit; extra == "test"
+Requires-Dist: pytest-ruff; extra == "test"
+Requires-Dist: ruff; extra == "test"
+Provides-Extra: prod
+Requires-Dist: pyvariantdb; extra == "prod"
+Provides-Extra: all
+Requires-Dist: pyvariantdb[test]; extra == "all"
+
+# dbSNP to Parquet Converter
+
+A python-package focused rewrite of [Weinstock's dbSNP](https://github.com/weinstockj/dbSNP_to_parquet) to parquet
+repository.
+This package allows convenient download, processing and access to data from dbSNP. A simple python interface
+can be used to work with the data once it is processed.
+
+## Installation
+
+`pyvariantdb` is available on PyPI and can be installed from there with the package management tool of choice. For
+development we use pixi:
+
+```bash
+# install pixi
+curl -fsSL https://pixi.sh/install.sh | sh
+pixi update && pixi install
+```
+
+## Usage
+
+We recommend to prepare the data from the command line before using the package since download and processing takes
+quit some time. Per default the data is stored at ~/.cache/pyvariantdb. This can be changed through the usage of
+environment variables:
+
+```bash
+export PYVARIANTDB_HOME = "/raid/cache/pyvariantdb"
+```
+
+Execution of the pipeline can be done with:
+
+```bash
+# activate pixi
+pixi shell -e default
+# download dbsnp
+pyvariantdb-download
+# transform the database to parquets
+pyvariantdb-make-dbsnp 
+```
+
+We aim to provide an easy interface to extract genomic coordinates from dbSNP. For this, the main functionality
+is extremely simple. Just provide the rs-identifier (with or without chromosome) and we fetch the respective
+coordindates. However, to achieve this we need to run the pipeline mentioned above.
+
+Extracting coordinates is simple:
+
+```python
+from pyvariantdb.lookup import SNPLookup
+
+lookup = SNPLookup()
+# P53 mutations, chromosome 17
+rsids = ["rs1042522", "rs17878362", "rs1800372"]
+df_all = lookup.query_all(rsids)
+df_chr = lookup.query_chromosome(rsids, "17")
+print(df_all)
+print(df_chr) 
+```
+
+## Processing Pipeline
+
+`pyvariantdb` offers some quality of life improvements for working with dbSNP and the original repository.
+The original pipeline remains the same:
+
+1. Downloads dbSNP data (GRCh38 build 156)
+2. Filters for SNVs only
+3. Converts chromosome contigs to standard naming
+4. Splits data by chromosome
+5. Creates Parquet lookup tables with RSID mappings
+
+## Output
+
+The script entrypoint generates the following files on-disk to the defined cache dir.
+
+- `dbSNP_156.bcf` - Full filtered BCF file
+- `dbSNP_156.chr*.bcf` - Per-chromosome BCF files
+- `dbSNP_156.chr*.lookup.parquet` - Per-chromosome RSID lookup tables
+- `dbSNP_156.lookup.parquet` - Combined RSID lookup table

pyvariantdb-1.1/pyvariantdb.egg-info/SOURCES.txt

@@ -0,0 +1,17 @@
+MANIFEST.in
+README.md
+pyproject.toml
+pyvariantdb/__init__.py
+pyvariantdb/const.py
+pyvariantdb/download.py
+pyvariantdb/lookup.py
+pyvariantdb.egg-info/PKG-INFO
+pyvariantdb.egg-info/SOURCES.txt
+pyvariantdb.egg-info/dependency_links.txt
+pyvariantdb.egg-info/entry_points.txt
+pyvariantdb.egg-info/requires.txt
+pyvariantdb.egg-info/top_level.txt
+pyvariantdb/assets/Snakefile
+pyvariantdb/assets/config.yaml
+pyvariantdb/assets/contig_map.tsv
+tests/test_lookup.py

pyvariantdb-1.1/pyvariantdb.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

pyvariantdb-1.1/pyvariantdb.egg-info/entry_points.txt

@@ -0,0 +1,4 @@
+[console_scripts]
+pyvariantdb-download = pyvariantdb.download:download_dbsnp
+pyvariantdb-make-dbsnp = pyvariantdb.scripts.dbsnp2parquet:main
+pyvariantdb-snp2parquet = pyvariantdb.scripts.convert:main

pyvariantdb-1.1/pyvariantdb.egg-info/requires.txt

@@ -0,0 +1,13 @@
+
+[all]
+pyvariantdb[test]
+
+[prod]
+pyvariantdb
+
+[test]
+pytest
+twine
+pre-commit
+pytest-ruff
+ruff

pyvariantdb-1.1/pyvariantdb.egg-info/top_level.txt

@@ -0,0 +1 @@
+pyvariantdb

pyvariantdb-1.1/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+