dima-cli 1.0.0

The command-line interface of DiMA.

What is DiMA?

Protein sequence diversity is one of the major challenges in the design of diagnostic, prophylactic and therapeutic interventions against viruses. DiMA is a tool designed to facilitate the dissection of protein sequence diversity dynamics for viruses. DiMA provides a quantitative measure of sequence diversity by use of Shannon’s entropy, applied via a user-defined k-mer sliding window. Further, the entropy value is corrected for sample size bias by applying a statistical adjustment. Additionally, DiMA further interrogates the diversity by dissecting the entropy value at each k-mer position to various diversity motifs. The distinct k-mer sequences at each position are classified into the following motifs based on their incidence. Index is the predominant sequence, and all other distinct k-mers are referred to as total variants, sub-classified into major variant (the predominant variant), minor variants (k-mers with incidence in between major and unique motifs) and unique variants (seen once in the alignment). Moreover, the description line of the sequences in the alignment can be formatted for inclusion of meta-data that can be tagged to the diversity motifs. DiMA enables comparative diversity dynamics analysis, within and between proteins of a virus species, and proteomes of different viral species.

Installation

OPTION 1

pip install dima-cli

OPTION 2

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

OPTION 3

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

OPTION 4

Download the latest distribution at:

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

Install using:

$ pip install dima-{version}.whl

Command-Line Usage

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

Linux

dima-cli -h

Windows

dima-cli.exe -h

Basic Usage

dima-cli -i sequences.fasta -o output.json -l 9

dima-cli -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.

dima-cli -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	dima-cli -h	Prints a summary of all available command-line arguments.
-i	String	N/A	dima-cli -i '/path/to/alignment.fasta'	Absolute path to the aligned sequences file in FASTA format.
-o	String	N/A	dima-cli -i '/path/to/alignment.fasta' -o output.json	Absolute path to the output JSON file.
-l	Integer	9	dima-cli -i '/path/to/alignment.fasta' -l 12	The length of the generated k-mers.
-s	Integer	10000	dima-cli -i '/path/to/alignment.fasta' -s 20000	Maximum number of samples use when calculating entropy.
-it	Integer	10	dima-cli -i '/path/to/alignment.fasta' -it 100	Maximum number of iterations used when calculating entropy.
-he	Boolean	False	dima-cli -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	dima-cli -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	dima-cli -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

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

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

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

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

Module Usage

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

from dima import Dima
Dima('/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.