gentk 1.0.0

This is a python toolkit for the 4D Genome Browser project. It includes a client, algorithms and datastructures for accessing a 4DGenomeBrowser database.

Creating an instance of a client

The main way to interact with the database is to create a client, then make calls through the client to the database hosted at the server. The server is defined by its url and port.

    import gentk

    # provide the URL and port when creating an instance
    client = gentk.client.client("http://127.0.0.1", "8000")

    # set the project
    client.project = "test.00"

API

• get_structure_arrays() Get a list of structure arrays from the server. The list is made of key, value pairs (see below).
• get_sequence_arrays() Get a list of sequence arrays from the server. The list is made of key, value pairs (see below).
• get_arrays(type) Get a list of all arrays from the server. The list is made of key, value pairs (see below).

    Example:
    arrays = client.get_arrays()

    return value has the following structure:
    [
        {
            'id': int,
            'name': string,
            'type': string
        },
        {
            'id': int,
            'name': string,
            'type': string
        },
        ,,,
    ]

• set_array(array, metadata) Set a new array on the server. Returns the id of the new array (integer)

    Example:
    metadata = {
                    "name": "test array", 
                    "type": "structure", 
                    "datatype": "int", 
                    "datadim": 1
                 }
   id = client.set_array([0, 1, 2, 3, 4], metadata)

• get_array(arrayID) Get an array from the server. Returns a json object.

    Example:

    result = client.get_array(id)

    return value has the following structure:
    {
        'name' : string,
        'type' : string,
        'version' : string (version of the array format)
        'data' {
            'type': string,
            'dim' : int,
            'values' : python data array
        }
    }

• get_contactmap(mapID) Get a contact map data structure.
• get_genes() Get the list of genes for a project.
• get_genes_for_segment(structureID, segID) Get a list of genes for a structure's segment.
• get_segments_for_gene(structureID, gene) Get a list of structure segments that a gene intersects.
• get_segment_ids(structureID) Return a list of segment IDs for a structure.
• get_structure(structureID) Get a structure. Return value is a list of segments.

    Example:

    structure = client.get_structure(id)

    return value has the following structure, which is a list of segments:
    [
        {
            'end'       : list of three floats,
            'length'    : int; length of segment,
            'segid'     : int,
            'start'     : list of three floats,
            'startid'   : int; start ID in the sequence
        },
        ...
    ]

Copyright (c) 2021 Los Alamos National Laboratory