pyvariantdb 1.3__tar.gz → 1.4__tar.gz

pyvariantdb-1.4/PKG-INFO

@@ -0,0 +1,256 @@
+Metadata-Version: 2.4
+Name: pyvariantdb
+Version: 1.4
+Summary: A python package to download, process and access dbSNP data.
+License: # Attribution-NonCommercial 4.0 International
+        
+        > *Creative Commons Corporation (“Creative Commons”) is not a law firm and does not provide legal services or legal advice. Distribution of Creative Commons public licenses does not create a lawyer-client or other relationship. Creative Commons makes its licenses and related information available on an “as-is” basis. Creative Commons gives no warranties regarding its licenses, any material licensed under their terms and conditions, or any related information. Creative Commons disclaims all liability for damages resulting from their use to the fullest extent possible.*
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+        > Creative Commons public licenses provide a standard set of terms and conditions that creators and other rights holders may use to share original works of authorship and other material subject to copyright and certain other rights specified in the public license below. The following considerations are for informational purposes only, are not exhaustive, and do not form part of our licenses.
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+        ## Creative Commons Attribution-NonCommercial 4.0 International Public License
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+        By exercising the Licensed Rights (defined below), You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution-NonCommercial 4.0 International Public License ("Public License"). To the extent this Public License may be interpreted as a contract, You are granted the Licensed Rights in consideration of Your acceptance of these terms and conditions, and the Licensor grants You such rights in consideration of benefits the Licensor receives from making the Licensed Material available under these terms and conditions.
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+        
+           6. __No endorsement.__ Nothing in this Public License constitutes or may be construed as permission to assert or imply that You are, or that Your use of the Licensed Material is, connected with, or sponsored, endorsed, or granted official status by, the Licensor or others designated to receive attribution as provided in Section 3(a)(1)(A)(i).
+        
+        b. ___Other rights.___
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+           1. Moral rights, such as the right of integrity, are not licensed under this Public License, nor are publicity, privacy, and/or other similar personality rights; however, to the extent possible, the Licensor waives and/or agrees not to assert any such rights held by the Licensor to the limited extent necessary to allow You to exercise the Licensed Rights, but not otherwise.
+        
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+        ### Section 3 – License Conditions.
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+        Your exercise of the Licensed Rights is expressly made subject to the following conditions.
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+        Where the Licensed Rights include Sui Generis Database Rights that apply to Your use of the Licensed Material:
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+        ### Section 8 – Interpretation.
+        
+        a. For the avoidance of doubt, this Public License does not, and shall not be interpreted to, reduce, limit, restrict, or impose conditions on any use of the Licensed Material that could lawfully be made without permission under this Public License.
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+        b. To the extent possible, if any provision of this Public License is deemed unenforceable, it shall be automatically reformed to the minimum extent necessary to make it enforceable. If the provision cannot be reformed, it shall be severed from this Public License without affecting the enforceability of the remaining terms and conditions.
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+        d. Nothing in this Public License constitutes or may be interpreted as a limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or You, including from the legal processes of any jurisdiction or authority.
+        
+        > Creative Commons is not a party to its public licenses. Notwithstanding, Creative Commons may elect to apply one of its public licenses to material it publishes and in those instances will be considered the “Licensor.” Except for the limited purpose of indicating that material is shared under a Creative Commons public license or as otherwise permitted by the Creative Commons policies published at [creativecommons.org/policies](http://creativecommons.org/policies), Creative Commons does not authorize the use of the trademark “Creative Commons” or any other trademark or logo of Creative Commons without its prior written consent including, without limitation, in connection with any unauthorized modifications to any of its public licenses or any other arrangements, understandings, or agreements concerning use of licensed material. For the avoidance of doubt, this paragraph does not form part of the public licenses.
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+        
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+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"
+Requires-Dist: grayskull; extra == "test"
+Provides-Extra: prod
+Requires-Dist: pyvariantdb; extra == "prod"
+Provides-Extra: all
+Requires-Dist: pyvariantdb[test]; extra == "all"
+Dynamic: license-file
+
+# 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_chr = lookup.query_chromosome(rsids, "17")
+df_genome = lookup.query_genome(rsids)
+print(df_chr)
+print(df_genome) 
+```
+
+## 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-1.3 → pyvariantdb-1.4}/README.md

@@ -49,10 +49,10 @@ 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) 
+df_genome = lookup.query_genome(rsids)
+print(df_chr)
+print(df_genome) 
 ```
 
 ## Processing Pipeline

{pyvariantdb-1.3 → pyvariantdb-1.4}/pyproject.toml

@@ -1,9 +1,10 @@
 [project]
 name = "pyvariantdb"
-version = "1.3"
+version = "1.4"
 description = "A python package to download, process and access dbSNP data."
 readme = "README.md"
 requires-python = ">=3.11"
+license = {file = "LICENSE"}
 
 [project.scripts]
 pyvariantdb-download = "pyvariantdb.download:download_dbsnp"

{pyvariantdb-1.3 → pyvariantdb-1.4}/pyvariantdb/const.py

@@ -8,7 +8,9 @@ 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 = Path(
+        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-1.4/pyvariantdb.egg-info/PKG-INFO

@@ -0,0 +1,256 @@
+Metadata-Version: 2.4
+Name: pyvariantdb
+Version: 1.4
+Summary: A python package to download, process and access dbSNP data.
+License: # Attribution-NonCommercial 4.0 International
+        
+        > *Creative Commons Corporation (“Creative Commons”) is not a law firm and does not provide legal services or legal advice. Distribution of Creative Commons public licenses does not create a lawyer-client or other relationship. Creative Commons makes its licenses and related information available on an “as-is” basis. Creative Commons gives no warranties regarding its licenses, any material licensed under their terms and conditions, or any related information. Creative Commons disclaims all liability for damages resulting from their use to the fullest extent possible.*
+        >
+        > ### Using Creative Commons Public Licenses
+        >
+        > Creative Commons public licenses provide a standard set of terms and conditions that creators and other rights holders may use to share original works of authorship and other material subject to copyright and certain other rights specified in the public license below. The following considerations are for informational purposes only, are not exhaustive, and do not form part of our licenses.
+        >
+        > * __Considerations for licensors:__ Our public licenses are intended for use by those authorized to give the public permission to use material in ways otherwise restricted by copyright and certain other rights. Our licenses are irrevocable. Licensors should read and understand the terms and conditions of the license they choose before applying it. Licensors should also secure all rights necessary before applying our licenses so that the public can reuse the material as expected. Licensors should clearly mark any material not subject to the license. This includes other CC-licensed material, or material used under an exception or limitation to copyright. [More considerations for licensors](http://wiki.creativecommons.org/Considerations_for_licensors_and_licensees#Considerations_for_licensors).
+        >
+        > * __Considerations for the public:__ By using one of our public licenses, a licensor grants the public permission to use the licensed material under specified terms and conditions. If the licensor’s permission is not necessary for any reason–for example, because of any applicable exception or limitation to copyright–then that use is not regulated by the license. Our licenses grant only permissions under copyright and certain other rights that a licensor has authority to grant. Use of the licensed material may still be restricted for other reasons, including because others have copyright or other rights in the material. A licensor may make special requests, such as asking that all changes be marked or described. Although not required by our licenses, you are encouraged to respect those requests where reasonable. [More considerations for the public](http://wiki.creativecommons.org/Considerations_for_licensors_and_licensees#Considerations_for_licensees).
+        
+        ## Creative Commons Attribution-NonCommercial 4.0 International Public License
+        
+        By exercising the Licensed Rights (defined below), You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution-NonCommercial 4.0 International Public License ("Public License"). To the extent this Public License may be interpreted as a contract, You are granted the Licensed Rights in consideration of Your acceptance of these terms and conditions, and the Licensor grants You such rights in consideration of benefits the Licensor receives from making the Licensed Material available under these terms and conditions.
+        
+        ### Section 1 – Definitions.
+        
+        a. __Adapted Material__ means material subject to Copyright and Similar Rights that is derived from or based upon the Licensed Material and in which the Licensed Material is translated, altered, arranged, transformed, or otherwise modified in a manner requiring permission under the Copyright and Similar Rights held by the Licensor. For purposes of this Public License, where the Licensed Material is a musical work, performance, or sound recording, Adapted Material is always produced where the Licensed Material is synched in timed relation with a moving image.
+        
+        b. __Adapter's License__ means the license You apply to Your Copyright and Similar Rights in Your contributions to Adapted Material in accordance with the terms and conditions of this Public License.
+        
+        c. __Copyright and Similar Rights__ means copyright and/or similar rights closely related to copyright including, without limitation, performance, broadcast, sound recording, and Sui Generis Database Rights, without regard to how the rights are labeled or categorized. For purposes of this Public License, the rights specified in Section 2(b)(1)-(2) are not Copyright and Similar Rights.
+        
+        d. __Effective Technological Measures__ means those measures that, in the absence of proper authority, may not be circumvented under laws fulfilling obligations under Article 11 of the WIPO Copyright Treaty adopted on December 20, 1996, and/or similar international agreements.
+        
+        e. __Exceptions and Limitations__ means fair use, fair dealing, and/or any other exception or limitation to Copyright and Similar Rights that applies to Your use of the Licensed Material.
+        
+        f. __Licensed Material__ means the artistic or literary work, database, or other material to which the Licensor applied this Public License.
+        
+        g. __Licensed Rights__ means the rights granted to You subject to the terms and conditions of this Public License, which are limited to all Copyright and Similar Rights that apply to Your use of the Licensed Material and that the Licensor has authority to license.
+        
+        h. __Licensor__ means the individual(s) or entity(ies) granting rights under this Public License.
+        
+        i. __NonCommercial__ means not primarily intended for or directed towards commercial advantage or monetary compensation. For purposes of this Public License, the exchange of the Licensed Material for other material subject to Copyright and Similar Rights by digital file-sharing or similar means is NonCommercial provided there is no payment of monetary compensation in connection with the exchange.
+        
+        j. __Share__ means to provide material to the public by any means or process that requires permission under the Licensed Rights, such as reproduction, public display, public performance, distribution, dissemination, communication, or importation, and to make material available to the public including in ways that members of the public may access the material from a place and at a time individually chosen by them.
+        
+        k. __Sui Generis Database Rights__ means rights other than copyright resulting from Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, as amended and/or succeeded, as well as other essentially equivalent rights anywhere in the world.
+        
+        l. __You__ means the individual or entity exercising the Licensed Rights under this Public License. Your has a corresponding meaning.
+        
+        ### Section 2 – Scope.
+        
+        a. ___License grant.___
+        
+           1. Subject to the terms and conditions of this Public License, the Licensor hereby grants You a worldwide, royalty-free, non-sublicensable, non-exclusive, irrevocable license to exercise the Licensed Rights in the Licensed Material to:
+        
+               A. reproduce and Share the Licensed Material, in whole or in part, for NonCommercial purposes only; and
+        
+               B. produce, reproduce, and Share Adapted Material for NonCommercial purposes only.
+        
+           2. __Exceptions and Limitations.__ For the avoidance of doubt, where Exceptions and Limitations apply to Your use, this Public License does not apply, and You do not need to comply with its terms and conditions.
+        
+           3. __Term.__ The term of this Public License is specified in Section 6(a).
+        
+           4. __Media and formats; technical modifications allowed.__ The Licensor authorizes You to exercise the Licensed Rights in all media and formats whether now known or hereafter created, and to make technical modifications necessary to do so. The Licensor waives and/or agrees not to assert any right or authority to forbid You from making technical modifications necessary to exercise the Licensed Rights, including technical modifications necessary to circumvent Effective Technological Measures. For purposes of this Public License, simply making modifications authorized by this Section 2(a)(4) never produces Adapted Material.
+        
+           5. __Downstream recipients.__
+        
+                A. __Offer from the Licensor – Licensed Material.__ Every recipient of the Licensed Material automatically receives an offer from the Licensor to exercise the Licensed Rights under the terms and conditions of this Public License.
+        
+                B. __No downstream restrictions.__ You may not offer or impose any additional or different terms or conditions on, or apply any Effective Technological Measures to, the Licensed Material if doing so restricts exercise of the Licensed Rights by any recipient of the Licensed Material.
+        
+           6. __No endorsement.__ Nothing in this Public License constitutes or may be construed as permission to assert or imply that You are, or that Your use of the Licensed Material is, connected with, or sponsored, endorsed, or granted official status by, the Licensor or others designated to receive attribution as provided in Section 3(a)(1)(A)(i).
+        
+        b. ___Other rights.___
+        
+           1. Moral rights, such as the right of integrity, are not licensed under this Public License, nor are publicity, privacy, and/or other similar personality rights; however, to the extent possible, the Licensor waives and/or agrees not to assert any such rights held by the Licensor to the limited extent necessary to allow You to exercise the Licensed Rights, but not otherwise.
+        
+           2. Patent and trademark rights are not licensed under this Public License.
+        
+           3. To the extent possible, the Licensor waives any right to collect royalties from You for the exercise of the Licensed Rights, whether directly or through a collecting society under any voluntary or waivable statutory or compulsory licensing scheme. In all other cases the Licensor expressly reserves any right to collect such royalties, including when the Licensed Material is used other than for NonCommercial purposes.
+        
+        ### Section 3 – License Conditions.
+        
+        Your exercise of the Licensed Rights is expressly made subject to the following conditions.
+        
+        a. ___Attribution.___
+        
+           1. If You Share the Licensed Material (including in modified form), You must:
+        
+               A. retain the following if it is supplied by the Licensor with the Licensed Material:
+        
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+        
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+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"
+Requires-Dist: grayskull; extra == "test"
+Provides-Extra: prod
+Requires-Dist: pyvariantdb; extra == "prod"
+Provides-Extra: all
+Requires-Dist: pyvariantdb[test]; extra == "all"
+Dynamic: license-file
+
+# 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_chr = lookup.query_chromosome(rsids, "17")
+df_genome = lookup.query_genome(rsids)
+print(df_chr)
+print(df_genome) 
+```
+
+## 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-1.3/PKG-INFO

@@ -1,96 +0,0 @@
-Metadata-Version: 2.4
-Name: pyvariantdb
-Version: 1.3
-Summary: A python package to download, process and access dbSNP data.
-Requires-Python: >=3.11
-Description-Content-Type: text/markdown
-License-File: LICENSE
-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"
-Requires-Dist: grayskull; extra == "test"
-Provides-Extra: prod
-Requires-Dist: pyvariantdb; extra == "prod"
-Provides-Extra: all
-Requires-Dist: pyvariantdb[test]; extra == "all"
-Dynamic: license-file
-
-# 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-1.3/pyvariantdb.egg-info/PKG-INFO

@@ -1,96 +0,0 @@
-Metadata-Version: 2.4
-Name: pyvariantdb
-Version: 1.3
-Summary: A python package to download, process and access dbSNP data.
-Requires-Python: >=3.11
-Description-Content-Type: text/markdown
-License-File: LICENSE
-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"
-Requires-Dist: grayskull; extra == "test"
-Provides-Extra: prod
-Requires-Dist: pyvariantdb; extra == "prod"
-Provides-Extra: all
-Requires-Dist: pyvariantdb[test]; extra == "all"
-Dynamic: license-file
-
-# 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