wugb-utils

Ths repository includes some utilities for Washington University Genome Browser (WUGB).

1. make_wugb_json.py

This script scans a web server's directory (based on servers dict), and saves a JSON file that includes all supported data files in this directory.

The output JSON file can be loaded directly into WUGB.

1.1 Syntax:

make_wugb_json.py [genome_type] [data_directory]

Two arguments are required by the script:

• genome_type, such as hg19 or hg38
• data_directory, which is the location of your data files

Two new files will be generated by the script:

• wugb.json: JSON file for WUGB
• wugb_url.txt: the URL of WUGB (also in standard output when the script is done)

1.2 Example

Suppose your data_directory is my_data, which has the following structure:

my_data/
├── d1
│   └── f1.bw
└── d2
    ├── f2.bw
    └── f3.bw

After you run:

make_wugb_json.py hg38 my_data

the structure of my_data will become:

my_data/
├── d1
│   └── f1.bw
├── d2
│   ├── f2.bw
│   └── f3.bw
├── wugb.json
└── wugb_url.txt