Metadata-Version: 1.1
Name: ndexutil
Version: 0.3.0a1
Summary: Unsupported NDEx utilities
Home-page: https://github.com/ndexbio/ndexutils
Author: The NDEx Project
Author-email: contact@ndexbio.org
License: BSD
Description: ndex-python-utilities
        =====================
        
        **Warning: This repository is for development and features may change.
        Please use this at your own risk.**
        
        
        Dependencies
        ------------
        
        * `ndex2 <https://pypi.org/project/ndex2>`_
        * `networkx <https://pypi.org/project/networkx>`_
        * `ndexutil <https://pypi.org/project/ndexutil>`_
        * `biothings_client <https://pypi.org/project/biothings-client>`_
        * `requests <https://pypi.org/project/requests>`_
        * `requests-toolbelt <https://pypi.org/project/requests_toolbelt>`_
        * `pandas <https://pypi.org/project/pandas>`_
        * `mygene <https://pypi.org/project/mygene>`_
        * `enum34 <https://pypi.org/project/enum34>`_
        * `jsonschema <https://pypi.org/project/jsonschema>`_
        * `urllib3 <https://pypi.org/project/urllib3>`_
        
        Compatibility
        -------------
        
        * Python 3.3+
        
        Installation
        ------------
        
        .. code-block::
        
           git clone https://github.com/ndexbio/ndexutils
           cd ndexutils
           make dist
           pip install dist/ndexutil*whl
        
        OR via `PyPI <https://pypi.org/ndexutils>`_
        
        .. code-block::
        
           pip install ndexutil
        
        
        TSV Loader
        ----------
        
        This module contains the Tab Separated Variable Loader (TSV Loader) which generates
        an `NDEx CX <http://www.home.ndexbio.org/data-model/>`_ file from a tab separated
        text file of edge data and attributes.
        
        To load data a load plan must be created. This plan tells the loader how to map the
        columns in the file to nodes, and edges. This load plan needs to validate against
        `this load plan JSON schema <https://github.com/ndexbio/ndexutils/blob/master/ndexutil/tsv/loading_plan_schema.json>`_
        
        **Example TSV file**
        
        .. code-block::
        
            SOURCE  TARGET  WEIGHT
            ABCD    AAA1    0.555
            GGGG    BBBB    0.305
        
        **SOURCE** is the source node, **TARGET** is target node
        
        A schema that could be:
        
        .. code-block::
        
            {
            "source_plan":
                {
                    "node_name_column": "SOURCE"
                },
                "target_plan":
                {
                    "node_name_column": "TARGET"
                },
                "edge_plan":
                {
                    "default_predicate": "unknown",
                    "property_columns": [
                      {
                        "column_name": "WEIGHT",
                        "attribute_name": "weight",
                        "data_type": "double"
                      }
                    ]
                }
            }
        
        
        
        Example below assumes the following:
        
        * **./loadplan.json** is the load plan in JSON format
        * **./style.cx** is a `NDEx CX <http://www.home.ndexbio.org/data-model/>`_ with a style.
        
        .. code-block::
        
            import ndex2
            from ndexutil.tsv.streamtsvloader import StreamTSVLoader
        
            # using ndex2 client library read CX file as NiceCXNetwork object
            style_network = ndex2.create_nice_cx_from_file('./style.cx')
        
            loader = StreamTSVLoader('./loadplan.json', style_network)
            with open('./input.tsv', 'r') as tsvfile:
                with open('./output.cx', 'w') as outfile:
                    loader.write_cx_network(tsvfile, outfile)
        
        
        Credits
        -------
        
        
        
        =======
        History
        =======
        
        0.3.0 2019-05-14
        ----------------
        
        * tsv2nicecx2.convert_pandas_to_nice_cx_with_load_plan now loads @context
          data into a @context network attribute instead of a separate aspect
        
        0.2.0 2019-04-01
        ----------------
        
        * StreamTSVLoader class added which enables loading of TSV data into
          in streaming format to handle loading of large networks
        
        
        
        
Keywords: network analysis biology
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Natural Language :: English
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3.6
