Hunana

A modular implementation of Hunana. A sub-module of ViVA.

The conserved sequences of the viral protein sequences are considered as candidates for vaccine design against continuously mutating viruses. Nonameric sequences from the viral genome are recognized and processed by human leukocyte antigens and T cell receptors. HUNANA is a command-line based tool which can provide a list of positions of conserved nonameric (kmer) sequences for a given viral protein sequence by utilizing Shannon’s entropy formula.

Installation

OPTION 1

pip install hunana

OPTION 2

pip install git+https://github.com/pu-sds/hunana.git

OPTION 3

git clone https://github.com/pu-sds/hunana.git
cd hunana
python setup.py install

OPTION 4

Download the latest distribution at:

https://github.com/pu-sds/hunana/releases/latest

Install using:

$ pip install hunana-{version}.whl

Command-Line Usage

Once installation is complete, an executable will be added to PATH which can be accessed as below:

Linux

hunana -h

Windows

hunana.exe -h

Basic Usage

hunana -i sequences.fasta -o output.json -l 9

hunana -i sequences.fasta | grep supports

Basic Usage Output (Example)

[
  {
    "position":1,
    "entropy":1.0002713744986218,
    "supports":2,
    "variants":[
      {
        "position":1,
        "sequence":"SKGKRTVDL",
        "count":1,
        "incidence":50.0,
        "motif_short":"I",
        "motif_long":"Index"
      },
      {
        "position":1,
        "sequence":"FHWLMLNPN",
        "count":1,
        "incidence":50.0,
        "motif_short":"Ma",
        "motif_long":"Major"
      }
    ],
    "kmer_types":{
      "incidence":50.0,
      "types":[
        "FHWLMLNPN"
      ]
    }
  }
]

Advanced Usage (Generate Variant Data)

The flag --he/--header along with the -f/--format header can be used to generate data for each variant using the metadata from the fasta sequence header.

hunana -i sequences.fasta -o output.json -he -f "(type)|(id)|(strain)"

Each componant (ex: id, strain, country, etc)of the header needs to be wrapped in brackets. Any separator (Ex: |, /, _, etc) can be used.

Advanced Usage Output (Example)

[
  {
    "position":1,
    "entropy":1.0001724373828909,
    "supports":2,
    "variants":[
      {
        "position":1,
        "sequence":"SKGKRTVDL",
        "count":1,
        "incidence":50.0,
        "motif_short":"I",
        "motif_long":"Index",
        "type":[
          "tr"
        ],
        "accession":[
          "A0A2Z4MTJ4"
        ],
        "strain":[
          "A0A2Z4MTJ4_9HIV2_Envelope_glycoprotein_gp160_OS_Human_immunodeficiency_virus_2_OX_11709_GN_env_PE_4_SV_1"
        ]
      },
      {
        "position":1,
        "sequence":"FHWLMLNPN",
        "count":1,
        "incidence":50.0,
        "motif_short":"Ma",
        "motif_long":"Major",
        "type":[
          "tr"
        ],
        "accession":[
          "A0A0K2GVL2"
        ],
        "strain":[
          "A0A2Z4MTJ4_9HIV2_Envelope_glycoprotein_gp160_OS_Human_immunodeficiency_virus_2_OX_11709_GN_env_PE_4_SV_1"
        ]
      }
    ],
    "kmer_types":{
      "incidence":50.0,
      "types":[
        "FHWLMLNPN"
      ]
    }
  }
]

Command-Line Arguments

More Examples

hunana -i sequences.fasta -o output.json -he -f "(ncbid)/(strain)/(host)/(country)"

hunana -i sequences.fasta -o output.json -he -f "(ncbid)/(strain)/(host)|(country)"

hunana -i sequences.fasta -o output.json -he -f "(ab)/(cde)/(fghi)/(jklm)"

hunana -i sequences.fasta -o output.json -he -f "(ab)/(cde)/(fghi)/(jklm) -no_header_error"

Module Usage

Hunana can also be imported and used within your Python projects as below:

from hunana import Hunana
Hunana('/path/to/sequence.fasta').run()

Module Parameters