gfe_client

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.