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        "author": "Justin Fear",
        "author_email": "justin.m.fear@gmail.com",
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        "description": "# Biometalib\n\nBiometalib is a set of useful libraries and tools for working with SRA biological metadata.\n\n## Installation\n\nThis library is designed for python 3+ and can be installed with `pip` or `conda`.\n\n### Pip\n\nBiometalib can be installed using pip.\n\n```bash\npip install -y biometalib\n```\n\nOr the latest version can be installed by pip.\n\n```bash\npip install git+https://github.com/jfear/sramongo\npip install git+https://github.com/jfear/biometalib\n```\n\n### Conda [Suggested]\n\nFirst make sure you have a working installation of Anaconda, I suggest\n[Miniconda](https://conda.io/miniconda.html).\n\n```bash\nconda install -c jfear biometalib\n```\n\n## Attribute Selector\n\nAttribute selector is a helper script for selecting which attributes you want\nto focus on for a project. The biological metadata submitted by users contain a\nvariety of different types of attributes. Sometimes these include things like\nmisspellings or different forms of a word, it also includes attributes that are\nunique to a single project. This tool is to be used to quickly curate these\ncolumns. Attribute selector uses a `YAML` formatted file to store attribute\ndecisions.\n\nIn the YAML file, **selected attributes** will be the keys. When merging\nmultiple attributes into a single **selected attribute** they will be stored as\nvalues. For example:\n\n```\nsex:\n- sex\n- Sex\n- gender\n```\n\nHere the **selected attribute** `sex` has the attributes `Sex` and `gender`\nassociated with it.  There is also a special **selected attribute** `ignore` that will store a list\nof attributes that you want to ignore.\n\nUsing the BioSample selection sheet I have created a starting YAML that can be\nused when running `attribute_selector`.\n\nTo run the attributes selector on my public version of the Biometa database type:\n\n```bash\n# Download example YAML\n$ wget -O my_attribute_selection.yaml https://raw.githubusercontent.com/jfear/biometalib/master/data/flybase_example.yaml\n$ attribute_selector --host mongo.geneticsunderground.com --port 27022 --db sra --username sra --password oliver --authenticationDatabase user-data --config my_attribute_selection.yaml\n```\n\n`attribute_selector` is an interactive command line tool. Iterates overall\nattribute column names that are not already **selected attributes** in the\nYAML. The current attribute is displayed in red. At the prompt you can type:\n\n* `k` to set the current attribute as a **selected attribute** [keep]\n* `r` to rename the current attribute, this will set the current attribute as\n  value of the renamed **selected attribute** [rename]\n* `i` adds current attribute to ignore list [ignore]\n* `e` show example values listed under the current attribute [example]\n* `s` show attributes with similar names (fuzzy string match). Here **selected attributes** will appear in yellow [similar]\n* `n` skip and go to the next attribute [next]\n* `quit` exit out of the program, but save progress.\n\n\n\n",
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        "license": "MIT license",
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        "name": "biometalib",
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        "summary": "A set of helper functions for working with biological metadata from the SRA.",
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