pyriandx 0.1.13

API wrapper for PierianDx web services

Pyriandx

Pyriandx is an API library for PierianDx genomic web services.

Getting started

Pyriandx can be used as a CLI tool OR a library. Oooh fancy!

Using the CLI

TL;DR

pyriandx --username [e-mail] --password h4x0r --institution institution-name --json case-file.json my-cool-vcf.vcf

Example case-file.json is in pyriandx/json/create_case.json.

PierianDX API client ::: API wrapper for PierianDx web services

Usage: 
   pyriandx [-hxv] [--username <username>] [--password <password>] [--output-dir <output-dir>] --institution <institution> --json <json-file> <target-vcf>

Options:
   -h, --help                      Prints this help and exit
   -v, --version                   Prints the version and exits
   -b, --base_url                  Base URL for PierianDX service [default: https://app.uat.pieriandx.com/cgw-api/v2.0.0].
   -u, --username=username         Username for PierianDX service, usually an email address. Overrides environment if it exists.
   -p, --password=password         Password for PierianDX service. Overrides environment if it exists.
   -j, --json                      JSON file with details for target
   -i, --institution=institution   Institution to use for API authentication
   -o, --output-dir=output-dir     Directory to place downloaded reports. [default: output]
   -x, --verbose                   Make output more verbose innit


Environment variables:
   DEBUG_HTTP         If defined, prints verbose information for all http transactions
   USERNAME           If defined, uses this as username for authenticating to PierianDX
   PASSWORD           If defined, uses this as password for authenticating to PierianDX
   BASE_URL           If defined, uses this as base URL for PierianDX service

Using as a module

Check the examples/ folder for some sweet example code.