How to Inspect a Data Package

Below is an example of using JBQ to explore a sample data package:

Make a folder

Create a folder for data, say "BioConnect_Data"

mkdir BioConnect_Data

Download JBQ Executable

Follow the instructions in How to Install to download the JBQ executable into the "BioConnect_Data" folder

Download a sample data package

Download the sample data package JAXDP00006X.zip and save it in the same folder as JBQ executable ("BioConnect_Data").

For unix, wget https://storage.googleapis.com/jax-genome-browser-track-public-website-data/jbq/JAXDP00006X.zip

The folder should look like this:

.
├── BioConnect_Data
│    ├── jbq
│    ├── JAXDP00006X.zip

This setup ensures that both the JBQ executable and the sample data package are correctly placed in the "BioConnect_Data" folder.

Read a data package from zip file

jbq read package JAXDP00006X.zip

output

jbq read package JAXDP00006X.zip

Data Package Root: "C:\Users\liangh\Desktop\BioConnect_Data"
Read Sucess:  JAXDP00006X.zip
  total number of triples: 15555

with added unzipped folder

.
├── BioConnect_Data
│    ├── jbq
│    ├── JAXDP00006X.zip
│    ├── JAXDP00006X

JBQ can read both zip file or data package folder. For zip file, JBQ just unzip it first.

show studies

jbq read package JAXDP00006X --show study

output

Study
├── Name: JAXST000001
├── Title: Body weights of "Three Bears" mice on control or high fat high sugar diet.
├── Description: Three inbred mouse strains, NZO/HlLTJ, CAST/EiJ, and C57BL/6J, with differing susceptibility to type 2 diabetes
│   were weighed weekly from age 4 weeks to sacrifice at 15 weeks. Starting at 6 weeks, half the animals per strain were fed
│   control diet, and the other half were fed high fat, high sugar diet (HFHS). The same animals were used in metabolic
│   phenotyping and RNA sequencing.
└── Comments:
    ├── Species: mouse
    └── Cube Aim : 3.1

The options for "--show" are: study, investigation, assay, file. To show all, use word "all" or "a"

show files

jbq read package JAXDP00006X --show file