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        "author": "MDU Bioinformatics",
        "author_email": "andersgs@gmail.com",
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        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Programming Language :: Python :: Implementation :: CPython",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "# MDU Python Tools\n\n[![CircleCI](https://circleci.com/gh/MDU-PHL/mdu-pytools.svg?style=svg)](https://circleci.com/gh/MDU-PHL/mdu-pytools) ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/mdu-pytools) ![PyPI](https://img.shields.io/pypi/v/mdu-pytools) ![PyPI - License](https://img.shields.io/pypi/l/mdu-pytools)\n\n- [MDU Python Tools](#mdu-python-tools)\n  - [Background](#background)\n  - [Tools](#tools)\n    - [mdu-merge-ngs-lanes](#mdu-merge-ngs-lanes)\n    - [mdu-sra-uploads](#mdu-sra-uploads)\n      - [Environmental variables that can be used to set options](#environmental-variables-that-can-be-used-to-set-options)\n  - [Development](#development)\n    - [Development environment](#development-environment)\n\n## Background\n\nSome simple tools in python for MDU\n\n## Tools\n\n### mdu-merge-ngs-lanes\n\nUse it to correctly merge lanes from an Illumina run into the a single FASTQ.\n\nGet help:\n\n```bash\nmdu-merge-ngs-lanes --help\n```\n\nBasic usage:\n\n```bash\nmdu-merge-ngs-lanes -i /path/to/fastq_folder -o /path/to/output > cmd.sh\n```\n\nAdvanced usage:\n\nYou can split the output to muliple subfolders of the output folder by adding `--subfolder`\nto the command line. The option can be used multiple times, and takes two space separated values as input:\n`path` `regex`. The `path` gives a name of the subfolder in the output folder, and the `regex` expression\ndetermines which samples go in that subfolder.\n\nFor instance, the command below will split samples starting the NTC in to a subfolder called `ntc`,\nwhile all other samples will be added to a subfolder called `data`.\n\n```bash\nmdu-merge-ngs-lanes -i /path/to/fastq -o /path/to/output --subfolder 'data' '(?!NTC).*' --subfolder 'ntc' '(?<=NTC).*' > cmd.sh\n```\n\n### mdu-sra-uploads\n\nUse to it to upload FASTQ data to NCBI SRA.\n\nRequires a file with tab-separated values of `MDU ID` and `AUSMDUID`. For example:\n\nmdu1\\tausmdu1\n\nmdu2\\tausmdu2\n\nGetting help:\n\n```bash\nmdu-sra-uploads --help\n```\n\n```bash\nUsage: mdu-sra-upload [OPTIONS] ISOLATES\n\nOptions:\n  -f, --folder TEXT         Folder on NCBI to upload. Used to find the reads\n                            when submitting via the SRA portal.  [default:\n                            mdu]\n  -r, --reads-folder TEXT   Where reads are located (uses MDU_READS env\n                            variable if available).\n  -k, --ascp-key TEXT       Path to ascp ssh upload key (uses ASCP_UPLOAD_KEY\n                            env variable if available). This can be obtained\n                            from the SRA Submission Portal.\n  -s, --sra-subfolder TEXT  SRA subfolder owned by you where data will copied\n                            to (uses SRA_SUBFOLDER env variable is available).\n  --help                    Show this message and exit.\n```\n\nBasic usage:\n\n```bash\ncd /path/for/upload\n# copy paste isolates.txt\nmdu-sra-uploads isolates.txt\n# when completing the submission, search for pre-uploaded files in the folder called mdu\n```\n\n\n\n#### Environmental variables that can be used to set options\n\n* `MDU_READS`: full path to where FASTQ data is stored\n* `ASCP_UPLOAD_KEY`: full path to where your Aspera NCBI upload key is located (obtain one from the SRA submission portal under the Aspera command line instructions)\n* `SRA_FOLDER`: path to your folder at SRA. Usually composed by your `email` plus an \"_\" and some random alphanumeric characters. This can be obtained from SRA submission portal under the Aspera command line instructions (e.g., `john.doe@doe.industries.com_qEWo9`).\n\n## Development\n\n### Development environment\n\nTo develop with the same environment use `vagrant` and `virtualbox`:\n\n```bash\nvagrant up\nvagrant ssh\n```\n\nOnce logged in to the VM, the shared folder is in `/vagrant`.\n\n\n",
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