HUNANA 1.0.7

HUNANA

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

Argument	Type	Default	Example	Description
-h	N/A	N/A	hunana -h	Prints a summary of all available command-line arguments.
-i	String	N/A	hunana -i '/path/to/alignment.fasta'	Absolute path to the aligned sequences file in FASTA format.
-o	String	N/A	hunana -i '/path/to/alignment.fasta' -o output.json	Absolute path to the output JSON file.
-l	Integer	9	hunana -i '/path/to/alignment.fasta' -l 12	The length of the generated k-mers.
-s	Integer	10000	hunana -i '/path/to/alignment.fasta' -s 20000	Maximum number of samples use when calculating entropy.
-it	Integer	10	hunana -i '/path/to/alignment.fasta' -it 100	Maximum number of iterations used when calculating entropy.
-he	Boolean	False	hunana -i '/path/to/alignment.fasta' -he -f '(type)|(accession)|(strain)|(country)'	Enables decoding of the FASTA headers to derive details for each generated k-mer.
-f	String	N/A	hunana -i '/path/to/alignment.fasta' -he -f '(type)|(accession)|(strain)|(country)'	The format of the FASTA header in the FASTA Multiple Sequence Alignment.
-no_header_error	Boolean	False	hunana -i '/path/to/alignment.fasta' -he -f '(type)|(accession)|(strain)|(country)' -no_header_error	Whether to raise an error if empty items are found in any of the FASTA headers.

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

Argument	Type	Default	Description
seqs	str, TextIOWrapper, StringIO	N/A	A file handle, a FASTA sequence wrapped in a handle, or a filepath.
kmer_len	int	9	The length of the kmers to generate.
header_decode	bool	False	Whether to use FASTA headers to derive kmer information.
header_format	str	N/A	The format of the header (ex: (id)|(species)|(country)).
json_result	bool	False	Whether the results should be returned in json format.
max_samples	int	10000	The maximum number of samples to use when calculating entropy.
iterations	int	10	The maximum number of iterations to use when calculating entropy.
no_header_error	bool	False	Whether to raise an error if empty items are found in any of the FASTA headers.