{
    "info": {
        "author": "Vladimir Rynkov",
        "author_email": "vrynkov@ucsd.edu",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 2 - Pre-Alpha",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: BSD License",
            "Natural Language :: English",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7"
        ],
        "description": "==========================\nNDEx STRING Content Loader\n==========================\n\n\n.. image:: https://img.shields.io/pypi/v/ndexstringloader.svg\n        :target: https://pypi.python.org/pypi/ndexstringloader\n\n.. image:: https://img.shields.io/travis/vrynkov/ndexstringloader.svg\n        :target: https://travis-ci.org/ndexcontent/ndexstringloader\n\n.. image:: https://coveralls.io/repos/github/ndexcontent/ndexstringloader/badge.svg?branch=master\n        :target: https://coveralls.io/github/ndexcontent/ndexstringloader?branch=master\n\n.. image:: https://readthedocs.org/projects/ndexstringloader/badge/?version=latest\n        :target: https://ndexstringloader.readthedocs.io/en/latest/?badge=latest\n        :alt: Documentation Status\n\n\nPython application for loading STRING data into `NDEx <http://ndexbio.org>`_.\n\nThis tool downloads and unpacks the `STRING <https://string-db.org/>`_ files below\n\n    `9606.protein.links.full.v11.0.txt.gz <https://stringdb-static.org/download/protein.links.full.v11.0/9606.protein.links.full.v11.0.txt.gz>`_\n\n    `human.name_2_string.tsv.gz <https://string-db.org/mapping_files/STRING_display_names/human.name_2_string.tsv.gz>`_\n\n    `human.entrez_2_string.2018.tsv.gz <https://stringdb-static.org/mapping_files/entrez/human.entrez_2_string.2018.tsv.gz>`_\n\n    `human.uniprot_2_string.2018.tsv.gz <https://string-db.org/mapping_files/uniprot/human.uniprot_2_string.2018.tsv.gz>`_\n\ngenerates a new tsv file, transforms it to CX, and uploads it to NDEx server. Duplicate edges\n(edges that have the same Source and Target nodes and the same value of :code:`combined_score`)\nare included to the generated tsv and CX files only once. Name of the newly generated network includes\nthe value of :code:`cutoffscore` argument, for example,\n:code:`STRING - Human Protein Links - High Confidence (Score >= 0.7)`. In case user didn't specify :code:`--update UUID`\nargument, then the network with this name gets over-written in case if already exists on NDEx server;\notherwise, a new network is created.\nSpecifying :code:`--update UUID` command line argument will over-write network with this UUID if it is found.\nIf not, then user is asked if (s)he wants to create a new network. When network is updated, only edges and nodes are\nchanged; network attributes are not modified.\n\n\n**1\\)** Below is an example of a record\nfrom `9606.protein.links.full.v11.0.txt.gz <https://stringdb-static.org/download/protein.links.full.v11.0/9606.protein.links.full.v11.0.txt.gz>`_\n\n.. code-block::\n\n   9606.ENSP00000261819 9606.ENSP00000353549 0 0 0 0 0 102 90 987 260 900 0 754 622 999\n\n\nTo generate a STRING network, the loader reads rows from that file one by one and compares the value of the last\ncolumn :code:`combined_score` with the value :code:`cutoffscore` argument.  The row is not added to the network generated in case\n:code:`combined_score` is less than the commad-line argument :code:`cutoffscore`.\n\n\n**2\\)** If :code:`combined_score` is no than less :code:`cutoffscore`, the loader process two first columns\n\n.. code-block::\n\n   column 1 - protein1 (9606.ENSP00000261819)\n   column 2 - protein2 (9606.ENSP00000353549)\n\nWhen processing first column :code:`protein1`, the script\n\nreplaces :code:`Ensembl Id` with a :code:`display name`, for example :code:`9606.ENSP00000261819` becomes :code:`ANAPC5`. Mapping of\ndisplay names to :code:`Enseml Ids` is found in\n`human.name_2_string.tsv.gz <https://string-db.org/mapping_files/STRING_display_names/human.name_2_string.tsv.gz>`_\n\nuses `human.uniprot_2_string.2018.tsv.gz <https://string-db.org/mapping_files/uniprot/human.uniprot_2_string.2018.tsv.gz>`_\nto create :code:`represents` value.  For example, :code:`represents` for :code:`9606.ENSP00000261819` is :code:`uniprot:Q9UJX4`\n\nuses `human.entrez_2_string.2018.tsv.gz <https://stringdb-static.org/mapping_files/entrez/human.entrez_2_string.2018.tsv.gz>`_\nto create list of aliases for the current protein.  Thus, list of aliases for :code:`9606.ENSP00000261819` is\n:code:`ncbigene:51433|ensembl:ENSP00000261819`\n\n**3\\)** The second column :code:`protein2` is processed the same way as :code:`column 1`.\n\n**4\\)**  In the generated tsv file :code:`9606.protein.links.tsv`, :code:`protein1` and :code:`protein2` values from the original file are replaced with\n\n.. code-block::\n\n   protein_display_name_1 represents_1 alias_1 protein_display_name_2 represents_2 alias_2\n\nSo, the original\n\n.. code-block::\n\n   9606.ENSP00000261819 9606.ENSP00000353549 0 0 0 0 0 102 90 987 260 900 0 754 622 999\n\nbecomes\n\n.. code-block::\n\n   ANAPC5 uniprot:Q9UJX4 ncbigene:51433|ensembl:ENSP00000261819 CDC16 uniprot:Q13042  ncbigene:8881|ensembl:ENSP00000353549 0 0 0 0 0 102 90 987 260 900 0 754 622 999\n\n\n**5\\)**  The generated tsv file :code:`9606.protein.links.tsv` is then transformed to CX :code:`9606.protein.links.cx`.\nThe default style defined in :code:`style.cx` distributed with this loader is applied to the\ngenerated network in case neither :code:`--style` nor :code:`--template` is specified.\nUser can specify style template file with either :code:`--style` argument or\nstyle template network UUID :code:`--template UUID_of_style_template_network`.\nSpecifying both :code:`--template` and :code:`--style` is not allowed.\n\n**6\\)**  :code:`9606.protein.links.cx` is then uploaded to NDEx server either replacing\nan existing network (in case :code:`--update UUID` is specified or network with this name already exists),\nor creating a new network.\n\n\nDependencies\n------------\n\n* ndex2\n* ndexutil\n\nCompatibility\n-------------\n\n* Python 3.3+\n\nInstallation\n------------\n\n.. code-block::\n\n   git clone https://github.com/ndexcontent/ndexstringloader\n   cd ndexstringloader\n   make dist\n   pip install dist/ndexloadstring*whl\n\n\nRun **make** command with no arguments to see other build/deploy options including creation of Docker image\n\n.. code-block::\n\n   make\n\nOutput:\n\n.. code-block::\n\n   clean                remove all build, test, coverage and Python artifacts\n   clean-build          remove build artifacts\n   clean-pyc            remove Python file artifacts\n   clean-test           remove test and coverage artifacts\n   lint                 check style with flake8\n   test                 run tests quickly with the default Python\n   test-all             run tests on every Python version with tox\n   coverage             check code coverage quickly with the default Python\n   docs                 generate Sphinx HTML documentation, including API docs\n   servedocs            compile the docs watching for changes\n   testrelease          package and upload a TEST release\n   release              package and upload a release\n   dist                 builds source and wheel package\n   install              install the package to the active Python's site-packages\n   dockerbuild          build docker image and store in local repository\n   dockerpush           push image to dockerhub\n\n\nConfiguration\n-------------\n\nThe **ndexloadstring.py** requires a configuration file to be created.\nThe default path for this configuration is :code:`~/.ndexutils.conf` but can be overridden with\n:code:`--conf` flag.\n\n**Configuration file**\n\nNetworks listed in **[network_ids]** section need to be visible to the **user**\n\n.. code-block::\n\n    [ndexstringloader]\n    user = joe123\n    password = somepassword123\n    server = dev.ndexbio.org\n\n\nNeeded files\n------------\n\nLoad plan is required for running this script.  **string_plan.json**  found at **ndexstringloader/ndexstringloader** can be used for this purpose.\n\n\nUsage\n-----\n\nFor information invoke :code:`ndexloadstring.py -h`\n\n**Example usage**\n\nHere is how this command can be run for **dev** and **prod** targets:\n\n.. code-block::\n\n   ndexloadstring.py --profile dev tmpdir/\n\n   ndexloadstring.py --profile prod tmpdir/\n\n\nVia Docker\n~~~~~~~~~~~~~~~~~~~~~~\n\n**Example usage**\n\n**TODO:** Add information about example usage\n\n\n.. code-block::\n\n   docker run -v `pwd`:`pwd` -w `pwd` vrynkov/ndexstringloader:0.1.0 ndexloadstring.py --conf conf # TODO Add other needed arguments here\n\n\nCredits\n-------\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n\n\n=======\nHistory\n=======\n\n0.2.3 (2019-09-13)\n------------------\n* If user loads the entire STRING network (i.e., runs the script with --cutoffscore 0), the name of the resulting netwpork should be \"STRING - Human Protein Links\", not \"STRING - Human Protein Links - High Confidence\".\n\n0.2.2 (2019-09-12)\n------------------\n* Added new featured specified by UD-577 Quick improvement for new String loader (added optional --update argument that allows to specify the UUID of a target network to update; added optional --template argument that allows to specify the UUID of a target network to use as style template, the update operation now only changes nodes and edges, but leaves network properties untouched).\n\n0.2.1 (2019-08-23)\n------------------\n* Improved README file.\n* Added new JUnit tests (JUnit test coverage is 87%).\n\n0.2.0 (2019-07-26)\n------------------\n* Removed duplicate edges. Every pair of connected nodes in STRING networks had the same edge duplicated (one edge going from A to B, and another going from B to A).  Since edges in STRING are not directed, we can safely remove half of them.\n\n* Added new arguments to command line:\n   optional --cutoffscore (default is 0.7) - used to filter on combined_score column. To include edges with combined_score of 800 or higher, --cutoffscore 0.8 should be specified\n\n   required --datadir specifies a working directory where STRING files will be downloaded to and processed style.cx file that contains style is supplied with the STRING loader and used by default. It can be overwritten with --style argument.\n\n0.1.0 (2019-03-13)\n------------------\n* First release on PyPI.\n\n\n",
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