diff --git a/.circleci/config.yml b/.circleci/config.yml new file mode 100644 index 0000000..47dee30 --- /dev/null +++ b/.circleci/config.yml @@ -0,0 +1,110 @@ +version: 2.1 +workflows: + build_and_deploy: + jobs: + - build: + filters: + tags: + only: /.*/ + - test-python-install: + version: "3.6" + requires: + - build + - test-python-install: + version: "3.7" + requires: + - build + - deploy: + requires: + - build + filters: + tags: + only: /[0-9]+(\.[0-9]+)*[ab]?/ + branches: + ignore: /.*/ +jobs: + build: + docker: + - image: circleci/python:3.6 + steps: + - checkout + - restore_cache: + key: v1-dependency-cache-{{ checksum "setup.py" }} + - run: + name: install python dependencies + command: | + python3 -m venv venv + . venv/bin/activate + pip install -e . + - save_cache: + key: v1-dependency-cache-{{ checksum "setup.py" }} + paths: + - "venv" + - run: + name: run tests + command: | + . venv/bin/activate + pip install -e . + pip install pytest + pytest + test-python-install: + parameters: + version: + type: string + default: latest + docker: + - image: circleci/python:3.6 + steps: + - checkout + - restore_cache: + key: v1-dependency-cache-{{ checksum "setup.py" }} + - run: + name: install python dependencies + command: | + python3 -m venv venv + . venv/bin/activate + pip install -e . + - save_cache: + key: v1-dependency-cache-{{ checksum "setup.py" }} + paths: + - "venv" + - run: + name: run tests + command: | + . venv/bin/activate + pip install -e . + pip install pytest + pytest + deploy: + docker: + - image: circleci/python:3.6 + steps: + - checkout + - restore_cache: + key: v1-dependency-cache-{{ checksum "setup.py" }} + - run: + name: install python dependencies + command: | + python3 -m venv venv + . venv/bin/activate + pip install -e . + - save_cache: + key: v1-dependency-cache-{{ checksum "setup.py" }} + paths: + - "venv" + - run: + name: init .pypirc + command: | + echo -e "[pypi]" >> ~/.pypirc + echo -e "username = simonw" >> ~/.pypirc + echo -e "password = $PYPI_PASSWORD" >> ~/.pypirc + - run: + name: create packages + command: | + python setup.py bdist_wheel + - run: + name: upload to pypi + command: | + . venv/bin/activate + pip install twine + twine upload dist/* diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..b87fae6 --- /dev/null +++ b/.gitignore @@ -0,0 +1,8 @@ +.venv +__pycache__/ +*.py[cod] +*$py.class +venv +.eggs +.pytest_cache +*.egg-info \ No newline at end of file diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..261eeb9 --- /dev/null +++ b/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS + + APPENDIX: How to apply the Apache License to your work. + + To apply the Apache License to your work, attach the following + boilerplate notice, with the fields enclosed by brackets "[]" + replaced with your own identifying information. (Don't include + the brackets!) The text should be enclosed in the appropriate + comment syntax for the file format. We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/README.md b/README.md new file mode 100644 index 0000000..3451ddd --- /dev/null +++ b/README.md @@ -0,0 +1,33 @@ +# genome-to-sqlite + +[![PyPI](https://img.shields.io/pypi/v/genome-to-sqlite.svg)](https://pypi.org/project/genome-to-sqlite/) +[![CircleCI](https://circleci.com/gh/dogsheep/genome-to-sqlite.svg?style=svg)](https://circleci.com/gh/dogsheep/genome-to-sqlite) +[![License](https://img.shields.io/badge/license-Apache%202.0-blue.svg)](https://github.com/dogsheep/genome-to-sqlite/blob/master/LICENSE) + +Import your genome into a SQLite database. + +## How to install + + $ pip install genome-to-sqlite + +## How to use + +First, export your genome. This tool has only been tested against 23andMe so far. You can request an export of your genome from https://you.23andme.com/tools/data/download/ + +Now you can convert the resulting `export.zip` file to SQLite like so: + + $ genome-to-sqlite export.zip genome.db + +A progress bar will be displayed. You can disable this using `--silent`. + +``` +Importing genome [#----------------] 5% 00:01:33 +``` + +You can explore the resulting data using [Datasette](https://datasette.readthedocs.io/) like this: + + $ datasette genome.db --config facet_time_limit_ms:1000 + +Bumping up the facet time limit is useful in order to enable faceting by chromosome: + +http://127.0.0.1:8001/genome/genome?_facet=chromosome&_sort=position diff --git a/genome_to_sqlite/__init__.py b/genome_to_sqlite/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/genome_to_sqlite/cli.py b/genome_to_sqlite/cli.py new file mode 100644 index 0000000..a213561 --- /dev/null +++ b/genome_to_sqlite/cli.py @@ -0,0 +1,44 @@ +import click +import os +import zipfile +import sqlite_utils +from .utils import convert_genome_text_to_sqlite + + +@click.command() +@click.argument( + "export_file", + type=click.Path(exists=True, file_okay=True, dir_okay=False, allow_dash=False), + required=True, +) +@click.argument( + "db_path", + type=click.Path(file_okay=True, dir_okay=False, allow_dash=False), + required=True, +) +@click.option("-s", "--silent", is_flag=True, help="Don't show progress bar") +def cli(export_file, db_path, silent): + """Import your genome into a SQLite database. EXPORT_FILE can be .zip or .txt + + More information: https://github.com/dogsheep/genome-to-sqlite + """ + try: + zf = zipfile.ZipFile(export_file) + except zipfile.BadZipFile: + # Assume it is text + fp = open(export_file, "rb") + file_length = os.path.getsize(export_file) + else: + # Ensure export.xml is in there + filenames = [zi.filename for zi in zf.filelist] + if len(filenames) != 1: + raise click.ClickException("Zip file does not contain a single text file") + filename = filenames[0] + fp = zf.open(filename) + file_length = zf.getinfo(filename).file_size + db = sqlite_utils.Database(db_path) + if silent: + convert_genome_text_to_sqlite(fp, db) + else: + with click.progressbar(length=file_length, label="Importing genome") as bar: + convert_genome_text_to_sqlite(fp, db, progress_callback=bar.update) diff --git a/genome_to_sqlite/utils.py b/genome_to_sqlite/utils.py new file mode 100644 index 0000000..0043710 --- /dev/null +++ b/genome_to_sqlite/utils.py @@ -0,0 +1,20 @@ +COLUMNS = ("rsid", "chromosome", "position", "genotype") + + +def convert_genome_text_to_sqlite(fp, db, progress_callback=None): + # Need to call progress_callback with number of bytes processed each time + if progress_callback is None: + progress_callback = lambda n: n + + def yield_rows(): + for line in fp.readlines(): + progress_callback(len(line)) + if line.startswith(b"#"): + continue + bits = line.decode("utf-8").strip().split("\t") + row = dict(zip(COLUMNS, bits)) + row["position"] = int(row["position"]) + yield row + + db["genome"].upsert_all(yield_rows(), pk="rsid") + db["genome"].create_index(["chromosome"], if_not_exists=True) diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..12443a4 --- /dev/null +++ b/setup.py @@ -0,0 +1,32 @@ +from setuptools import setup +import os + +VERSION = "0.1" + + +def get_long_description(): + with open( + os.path.join(os.path.dirname(os.path.abspath(__file__)), "README.md"), + encoding="utf8", + ) as fp: + return fp.read() + + +setup( + name="genome-to-sqlite", + description="Import your genome into a SQLite database", + long_description=get_long_description(), + long_description_content_type="text/markdown", + author="Simon Willison", + url="https://github.com/dogsheep/genome-to-sqlite", + license="Apache License, Version 2.0", + version=VERSION, + packages=["genome_to_sqlite"], + entry_points=""" + [console_scripts] + genome-to-sqlite=genome_to_sqlite.cli:cli + """, + install_requires=["sqlite-utils"], + extras_require={"test": ["pytest"]}, + tests_require=["genome-to-sqlite[test]"], +) diff --git a/tests/example.txt b/tests/example.txt new file mode 100644 index 0000000..dcd3b96 --- /dev/null +++ b/tests/example.txt @@ -0,0 +1,7 @@ +# File starts with multiple lines of comments... +# +# rsid chromosome position genotype +rs12564807 1 326472 AA +rs3131972 1 583459 GG +rs1488288 1 876634 CC +rs12124819 1 947369 GG diff --git a/tests/export.xml b/tests/export.xml new file mode 100644 index 0000000..b310870 --- /dev/null +++ b/tests/export.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/test_genome_to_sqlite.py b/tests/test_genome_to_sqlite.py new file mode 100644 index 0000000..974e102 --- /dev/null +++ b/tests/test_genome_to_sqlite.py @@ -0,0 +1,55 @@ +from click.testing import CliRunner +from genome_to_sqlite import cli, utils +import pytest +import sqlite_utils +import pathlib +import zipfile + + +@pytest.fixture +def text_path(): + return str(pathlib.Path(__file__).parent / "example.txt") + + +@pytest.fixture +def db(text_path): + db = sqlite_utils.Database(":memory:") + utils.convert_genome_text_to_sqlite(open(text_path, "rb"), db) + return db + + +def test_conversion(db): + assert ["genome"] == db.table_names() + rows = list(db["genome"].rows) + assert [ + {"rsid": "rs12564807", "chromosome": "1", "position": 326472, "genotype": "AA"}, + {"rsid": "rs3131972", "chromosome": "1", "position": 583459, "genotype": "GG"}, + {"rsid": "rs1488288", "chromosome": "1", "position": 876634, "genotype": "CC"}, + {"rsid": "rs12124819", "chromosome": "1", "position": 947369, "genotype": "GG"}, + ] == rows + + +def test_help(): + result = CliRunner().invoke(cli.cli, ["--help"]) + assert result.output.startswith("Usage: cli") + + +def test_cli_parses_zip(text_path, tmpdir): + db_path = str(tmpdir / "output.db") + # Put the example in a zip file + zip_path = str(tmpdir / "genome.zip") + with zipfile.ZipFile(str(zip_path), "w") as z: + z.write(text_path, "genome.txt") + # Now use CLI tool to import that zip file + result = CliRunner().invoke(cli.cli, [zip_path, db_path]) + assert 0 == result.exit_code + db = sqlite_utils.Database(db_path) + assert ["genome"] == db.table_names() + + +def test_cli_parses_text(text_path, tmpdir): + db_path = str(tmpdir / "output.db") + result = CliRunner().invoke(cli.cli, [text_path, db_path]) + assert 0 == result.exit_code + db = sqlite_utils.Database(db_path) + assert ["genome"] == db.table_names()