{ "info": { "author": "Eike J. Steinig", "author_email": "eikejoachim.steinig@my.jcu.edu.au", "bugtrack_url": null, "classifiers": [], "description": "## DartQC\n### Quality Control Pipeline\n\nCommand line pipeline to facilitate quality control of SNP data from Diversity Array Technologies (DArT). This version is a re-write of the original scripts aiming to be somewhat more user-friendly and executable on JCU's HPC.\n\n#### Install\n\n`pip install dartqc`\n\n#### How to use DartQC\n\nThis section provides a brief guide of how to install and use the pipeline components. This assumes you are using a Bash shell on a local Unix system or the JCU's HPC (Zodiac).\n\n1. [Install DartQC](https://github.com/esteinig/dartQC/blob/master/readme/install.md)\n2. [Task: prepare](https://github.com/esteinig/dartQC/blob/master/readme/task.prepare.md)\n3. [Task: process](https://github.com/esteinig/dartQC/blob/master/readme/task.process.md)\n4. [Task: filter](https://github.com/esteinig/dartQC/blob/master/readme/task.filter.md)\n5. [DartQC on Zodiac]()\n\n#### Tasks\n\nDartQC has a hierarchical parser structure that allows you to set global options and execute a task (prepare, process, filter) with its own specific arguments:\n\n```\ndartqc --help\n\ndartqc prepare --help\ndartqc process --help\ndartqc filter -- help\n```\n\nGlobal arguments are specified before the command for a task, like this:\n\n**`dartqc`**`--project example --output_path ./example`**`prepare`**`--file example_data.csv`\n\n\n#### Quick Start\n\nExample workflow without pre-processing from Excel or CSV:\n\n```\nsource activate dartqc\n\n# CSV\ndartqc prepare --file example.csv\n# Excel\ndartqc prepare --file example.xlsx --sheet double_row_snps\n\ndartqc filter --call example.csv --call_scheme example_scheme.json --maf 0.02 --clusters\n\nsource deactivate\n```\n\nExample workflow with pre-processing:\n\n```\nsource activate dartqc\n\ndartqc prepare --file calls.csv\ndartqc prepare --file raw.csv\n\ndartqc filter -c calls.csv --call_scheme calls_scheme.json -r raw.csv --raw_scheme raw_scheme.json --read_threshold 7\n\ndartqc filter --processed ./example --maf 0.02 --call_rate 0.7 --duplicates --clusters\n\nsource deactivate\n```\n\n---\n\n

\n \n

\n\n---\n\n### Contact\n\nIf you find any bugs, please submit an issue for this repository on GitHub.\n\n\n\n", "description_content_type": null, "docs_url": null, "download_url": "http://github.com/esteinig/dartqc/archive/0.1.5.tar.gz", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "http://github.com/esteinig/dartqc", "keywords": null, "license": "MIT", "maintainer": null, "maintainer_email": null, "name": "dartqc", "package_url": "https://pypi.org/project/dartqc/", "platform": "UNKNOWN", "project_url": "https://pypi.org/project/dartqc/", "project_urls": { "Download": "http://github.com/esteinig/dartqc/archive/0.1.5.tar.gz", "Homepage": "http://github.com/esteinig/dartqc" }, "release_url": "https://pypi.org/project/dartqc/0.1.5/", "requires_dist": null, "requires_python": null, "summary": "Quality control for SNP data from Diversity Array Technologies (DArT)", "version": "0.1.5" }, "last_serial": 2899506, "releases": { "0.1": [ { "comment_text": "", "digests": { "md5": "50adc403fbb801eafe215d28596bb507", "sha256": "1be0141a847600c437e8b832670579817f080c855c75322026d153335d5f1930" }, "downloads": -1, "filename": "dartqc-0.1.tar.gz", "has_sig": false, "md5_digest": "50adc403fbb801eafe215d28596bb507", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 22264, "upload_time": "2017-05-25T00:15:28", "url": "https://files.pythonhosted.org/packages/0f/32/63d4f6a3dff25a9a98d22cec346c3889e2e0f1f3e4dc64669f39478f91a3/dartqc-0.1.tar.gz" } ], "0.1.1": [ { "comment_text": "", "digests": { "md5": "b3ea42dbbd42e13bff496e370cb811cc", "sha256": "f5e0e947126ca4da007f26f6f46ae74e42e24b6a86ed7576839f2c83571396d7" }, "downloads": -1, "filename": "dartqc-0.1.1.tar.gz", "has_sig": false, "md5_digest": "b3ea42dbbd42e13bff496e370cb811cc", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 22775, "upload_time": "2017-05-25T01:08:33", "url": "https://files.pythonhosted.org/packages/bd/47/117c2d11a9d064730f30d861b3ad9cafe37a1ac5b66583cd4a03d30e3816/dartqc-0.1.1.tar.gz" } ], "0.1.2": [ { "comment_text": "", "digests": { "md5": "674bbe882b629a1361a586303084e95f", "sha256": "57cdc429fe1f0b40b6150aa775850399597e23c7e204544ed648862fd5b6c5ae" }, "downloads": -1, "filename": "dartqc-0.1.2.tar.gz", "has_sig": false, "md5_digest": "674bbe882b629a1361a586303084e95f", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 23279, "upload_time": "2017-05-25T02:00:07", "url": "https://files.pythonhosted.org/packages/8b/80/801cb91701f8e44340335185a982a5f77bad04778b1d8c28117790759310/dartqc-0.1.2.tar.gz" } ], "0.1.3": [ { "comment_text": "", "digests": { "md5": "cbb6236e6f9fdcc86ac1be30630ab383", "sha256": "701ea8c68428b91a22b061ffd40ca4b7323a7b899eaacdf9055ea3af3b920e00" }, "downloads": -1, "filename": "dartqc-0.1.3.tar.gz", "has_sig": false, "md5_digest": "cbb6236e6f9fdcc86ac1be30630ab383", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 24310, "upload_time": "2017-05-25T04:56:57", "url": "https://files.pythonhosted.org/packages/ac/2c/30816cb8edcb1cf9871b538462d3e6f956a836952b930d9313f8e525e165/dartqc-0.1.3.tar.gz" } ], "0.1.4": [ { "comment_text": "", "digests": { "md5": "5d73125d4dca728d12f71144339c1312", "sha256": "4e0629b0f8582832f05872b3bf3a76140940fd88688b98ff6c3833ae3c900349" }, "downloads": -1, "filename": "dartqc-0.1.4.tar.gz", "has_sig": false, "md5_digest": "5d73125d4dca728d12f71144339c1312", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 24327, "upload_time": "2017-05-25T06:03:51", "url": "https://files.pythonhosted.org/packages/86/ba/b6fb826669f5d11accaeb8bb37364bb682d290c419a1bf335cae83f38087/dartqc-0.1.4.tar.gz" } ], "0.1.5": [ { "comment_text": "", "digests": { "md5": "b9ff4cef34b5e3a80406dfd2b7798024", "sha256": "75e64779a4674c5df7b235f2bb8ff2fa13f07bc380344cecde6a1edd8e4a314c" }, "downloads": -1, "filename": "dartqc-0.1.5.tar.gz", "has_sig": false, "md5_digest": "b9ff4cef34b5e3a80406dfd2b7798024", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 24961, "upload_time": "2017-05-26T03:19:54", "url": "https://files.pythonhosted.org/packages/a3/1f/0aaf9fdf9f079b989b5f8d229d12cfd6eae9b8ccd85e0490c6ed8b81dcd7/dartqc-0.1.5.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "b9ff4cef34b5e3a80406dfd2b7798024", "sha256": "75e64779a4674c5df7b235f2bb8ff2fa13f07bc380344cecde6a1edd8e4a314c" }, "downloads": -1, "filename": "dartqc-0.1.5.tar.gz", "has_sig": false, "md5_digest": "b9ff4cef34b5e3a80406dfd2b7798024", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 24961, "upload_time": "2017-05-26T03:19:54", "url": "https://files.pythonhosted.org/packages/a3/1f/0aaf9fdf9f079b989b5f8d229d12cfd6eae9b8ccd85e0490c6ed8b81dcd7/dartqc-0.1.5.tar.gz" } ] }