Metadata-Version: 1.1
Name: quilt
Version: 0.1.9
Summary: Quilt Python API https://quiltdata.com
Home-page: https://github.com/quiltdata/python-api
Author: quiltdata
Author-email: founders@quiltdata.io
License: LICENSE.txt
Download-URL: https://github.com/quiltdata/python-api/tarball/0.1.8
Description: .. image:: https://travis-ci.org/quiltdata/python-api.svg?branch=master
            :target: https://travis-ci.org/quiltdata/python-api
        .. image:: https://img.shields.io/badge/python-2.7%2C%203.4%2C%203.5-blue.svg
        
        Python
        ======
        
        The Quilt Python connector uses the Quilt REST API and SQL Alchemy
        (http://docs.sqlalchemy.org/), if installed, to access and update data
        sets in Quilt. Quilt tables are available as dictionaries or Pandas
        (http://pandas.pydata.org/) DataFrames.
        
        The Quilt Python connector is available via PyPI:
        https://pypi.python.org/pypi/quilt
        
        .. code:: python
        
            pip install quilt
        
        
        Connection
        ----------
        
        To use the Quilt Python connector, add this repository to your
        PYTHONPATH and import quilt.
        
        Connect to Quilt by creating a Connection object:
        
        .. code:: python
        
            import quilt
            connection = quilt.Connection(username=None)
            Quilt username: *enter your username*
            Password: *enter your password*
        
        The connection will contain a list of your Quilt tables:
        
        .. code:: python
        
            connection.tables
        
        Search for Data Sets
        ~~~~~~~~~~~~~~~~~~~~
        
        You can also find tables by searching your own tables and Quilt’s public
        data sets
        
        .. code:: python
        
            connection.search('term')
        
        Get Table
        ~~~~~~~~~
        
        Get a table by Table id using get\_table:
        
        .. code:: python
        
            t = connection.get_table(1234)
        
        Create a New Table
        ~~~~~~~~~~~~~~~~~~
        
        Using the connection, you can create new tables in Quilt. To create an
        empty table:
        
        .. code:: python
        
            t = connection.create_table(name, description)
        
        To create a table from an input file:
        
        .. code:: python
        
            t = connection.create_table(name, description, inputfile=path_to_input_file)
        
        Or, to create a new table from a DataFrame:
        
        .. code:: python
        
            t = connection.save_df(df, name, description="table description")
        
        
        
        Table
        -----
        
        Each Table object has a list of Columns
        
        .. code:: python
        
            mytable.columns
        
        After the columns have been fetched, columns are available as table
        attributes.
        
        .. code:: python
        
            mytable.column1
        
        Accessing Table Data
        ~~~~~~~~~~~~~~~~~~~~
        
        Tables are iterable. To access table data:
        
        .. code:: python
        
            for row in mytable:
                print(row)
        
        Search
        ^^^^^^
        
        Search for matching rows in a table by calling search.
        
        .. code:: python
        
            for row in mytable.search('foo'):
                print(row)
        
        Order By
        ^^^^^^^^
        
        Sort the table by any column or set of columns. You can set the ordering
        by passing a string that is the column’s field (name in the database).
        
        .. code:: python
        
            mytable.order_by('column1')
        
        You can find column field names with their “.field” attribute:
        
        .. code:: python
        
            mytable.order_by(mytable.column1.field)
        
        You can sort by multiple columns by passing a list of fields.
        
        .. code:: python
        
            mytable.order_by(['column2', 'column1'])
        
        To sort in descending order, add a “-” in front of the column field
        name:
        
        .. code:: python
        
            mytable.order_by('-column1')
        
        Limit
        ^^^^^
        
        Limit the number of rows returned by calling limit(number\_of\_rows).
        
        Putting it all together
        ^^^^^^^^^^^^^^^^^^^^^^^
        
        Search, order\_by and limit can be combined to return just the data you
        want to see. For example, to return the top 2 finishers with the name
        Sally from a table of race results (race\_results: [name\_000,
        time\_001]), you could write:
        
        .. code:: python
        
            for result in race_results.search('Sally').order_by('-time_001').limit(2):
                print(row)
        
        Pandas DataFrame
        ~~~~~~~~~~~~~~~~
        
        Access a table’s data as a Pandas DataFrame by calling mytable.df()
        
        You can also combine the querying methods above to access particular
        rows.
        
        .. code:: python
        
            race_results.search('Sally').order_by('-time\_001').limit(2).df()
        
        Gene Math
        ~~~~~~~~~
        
        Quilt supports intersect and subtract for tables that store genomic
        regions. Those operations assume that tables have columns storing:
        Chromsome, start and end. The function get\_bed\_cols tries to infer
        those columns based on column names.
        
        If the guessing fails, or to override the guess, set the chromosome,
        start, end columns explicitly with set\_bed\_cols.
        mytable.set\_bed\_cols(mytable.chr\_001, mytable.start\_002,
        mytable.end\_003)
        
        Once the bed columns are set for both tables, they can be intersected
        and subtracted.
        
        .. code:: python
        
            result = tableA.intersect(tableB)
            result = tableA.intersect_wao(tableB)
            result = tableA.subtract(tableB)
        
        
        Development
        -----------
        
        Tests run with:
        
        .. code:: python
        
            pip install -r requirements.txt
            pip install pytest pytest-cov
            pytest --cov=quilt/ tests
        
Keywords: quiltdata api social shareable data platform
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
