Light

nmdp-bioinformatics / act-client Goto Github PK

View Code? Open in Web Editor NEW

1.0 5.0 3.0 71 KB

Python client for working with the ACT service

License: GNU Lesser General Public License v3.0

Makefile 2.66% Python 83.34% Jupyter Notebook 14.00%

act-client's Introduction

gfe_client

Documentation Status

Updates

Python client for calling the ACT service

Free software: LGPL 3.0
Documentation: https://gfe-client.readthedocs.io.

Usage

To annotated a sequence initialize a new BioSeqAnn object and then pass the sequence to the annotate method. The sequence must be a Biopython Seq. The locus of the sequence is not required but it will improve the accuracy of the annotation.

  import gfe_client
  api = gfe_client.TypeSeqApi()
  response = api.typeseq_get(seq, imgthla_version="3.31.0")


You must have `act-service`_ running at localhost (port=80).

CLI

usage: gfecli [-h] -i FILE [-l LOCUS] [-d DBVERSION] [-a ACTSERVICE] [-f] [-v]

optional arguments:
  -h, --help            show this help message and exit
  -i FILE, --file FILE  input file
  -l LOCUS, --locus LOCUS
                        HLA locus
  -d DBVERSION, --dbversion DBVERSION
                        IMGT/HLA dbversion
  -a ACTSERVICE, --actservice ACTSERVICE
                        URL for ACT service
  -f, --features        Return all features
  -v, --verbose         Option for running in verbose

Annotations

{
    "features": [
     {
        "accession": 2,
        "rank": 6,
        "sequence": "ATAGAAAAGGAGGGAGCTACTCTCAGGCTGCAA",
        "term": "exon"
      },
      {
        "accession": 1,
        "rank": 6,
        "sequence": "GTAAGTATGAAGGAGGCTGATGCCTGAGGTCCTTGGGATATTGTGTTTGGGAGCCCATGGGGGAGCTCACCCACCCCACAATTCCTCCTCTAGCCACATCTTCTGTGGGATCTGACCAGGTTCTGTTTTTGTTCTACCCCAG",
        "term": "intron"
      },
      {
        "accession": 1,
        "rank": 7,
        "sequence": "GCAGTGACAGTGCCCAGGGCTCTGATGTGTCTCTCACAGCTTGTAAAG",
        "term": "exon"
      }
    ],
     "hla": "HLA-A*02:01:01:12",
     'gfe': 'HLA-Aw2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-4'
}

Install

pip install gfe-client

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

act-client's People

Contributors

Stargazers

Watchers

Forkers

mhalagan bmatern m-haziq

act-client's Issues

The usage code provided in README has typo

NameError: name 'typeseq_get' is not defined.

There should be a nice way to update act-client/gfe_client/configuration.py

The file act-client/gfe_client/configuration.py can be changed to set the configuration for connecting with act-service. Being a public package, there should be a smooth way or non-code way to change this configuration. This is open for discussion, can be done through some ENV VARIABLE or some other way maybe etc.

The Usage Code in README should explicitly indicate that it requires act-service running

The usage code provided in the README tries to connect with the act-service on localhost, which fails obviously if act-service is not running on localhost, this part should be mentioned explicitly.

api.typeseq_get(seq, imgthla_version="3.31.0") in README gives error

While trying the README on local, the following line gives error:
api.typeseq_get(seq, imgthla_version="3.31.0")

Security: Upgrade pyaml

Set pyaml to

pyyaml>=4.2b1

Same as #6

Recommend Projects

React

A declarative, efficient, and flexible JavaScript library for building user interfaces.
Vue.js

🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
Typescript

TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
TensorFlow

An Open Source Machine Learning Framework for Everyone
Django

The Web framework for perfectionists with deadlines.
Laravel

A PHP framework for web artisans
D3

Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

javascript

JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
web

Some thing interesting about web. New door for the world.
server

A server is a program made to process requests and deliver data to clients.
Machine learning

Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Visualization

Some thing interesting about visualization, use data art
Game

Some thing interesting about game, make everyone happy.

Recommend Org

Facebook

We are working to build community through open source technology. NB: members must have two-factor auth.
Microsoft

Open source projects and samples from Microsoft.
Google

Google ❤️ Open Source for everyone.
Alibaba

Alibaba Open Source for everyone
D3

Data-Driven Documents codes.
Tencent

China tencent open source team.