dima-cli 2.1.3_beta

A command-line tool that analyses the diversity and motifs of protein sequences

DiMA - Diversity Motif Analyser

Table of Contents

• What is DiMA?
• Installation
• Basic Usage
  • Shell Command
  • Python
  • Results
• Advance Usage
  • Shell Command
  • Python
  • Results
• Command-Line Arguments
• Module Parameters

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: The predominant sequence.
• Major: The sequence with the second highest incidence after the Index.
• Minor: Kmers with incidence in between major and unique motifs
• Unique: Kmers which are only seen once in a particular kmer position.

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

pip install dima-cli

Basic Usage

Shell Command

dima-cli -i aligned_sequences.afa -o results.json

Python

from dima import Dima
results = Dima(sequences="aligned_sequences.afa").run()

Results

{
   "sequence_count":203,
   "support_threshold":30,
   "low_support_count":15,
   "protein_name":"Unknown Protein",
   "kmer_length":9,
   "results":[
      {
         "position":1,
         "low_support":false,
         "entropy":0.8383740426713246,
         "support":124,
         "distinct_variants_count":4,
         "distinct_variants_incidence":3.2258062,
         "variants":[
            {
               "sequence":"MKTIIALSC",
               "count":2,
               "incidence":1.6129031,
               "motif_short":"Mi",
               "motif_long":"Minor",
               "metadata":null
            },
            {
               "sequence":"MKTIIALSH",
               "count":3,
               "incidence":2.4193547,
               "motif_short":"Mi",
               "motif_long":"Minor",
               "metadata":null
            },
            {
               "sequence":"METISLISM",
               "count":1,
               "incidence":0.80645156,
               "motif_short":"U",
               "motif_long":"Unique",
               "metadata":null
            },
            {
               "sequence":"MKNIIALSY",
               "count":13,
               "incidence":10.4838705,
               "motif_short":"Ma",
               "motif_long":"Major",
               "metadata":null
            },
            {
               "sequence":"MKTIIALSY",
               "count":105,
               "incidence":84.67742,
               "motif_short":"I",
               "motif_long":"Index",
               "metadata":null
            }
         ]
      }
   ]
}

Advance Usage

Shell Command

dima-cli -i aligned_sequences.afa -o results.json -f "accession|strain|country|date"

Python

from dima import Dima
results = Dima(sequences="aligned_sequences.afa", header_format="accession|strain|country|date").run()

Results

{
  "sequence_count": 3,
  "support_threshold": 30,
  "low_support_count": 18,
  "protein_name": "Unknown Protein",
  "kmer_length": 9,
  "results": [
    {
      "position": 1,
      "low_support": true,
      "entropy": 0.0,
      "support": 3,
      "distinct_variants_count": 0,
      "distinct_variants_incidence": 0.0,
      "variants": [
        {
          "sequence": "MSASKEIKS",
          "count": 3,
          "incidence": 100.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": {
            "accession": {
              "AYD75325.1": 1,
              "QEP52131.1": 1,
              "AYD75365.1": 1
            },
            "strain": {
              "Sierra Leone": 3
            },
            "date": {
              "2012": 1,
              "1980": 1,
              "1979": 1
            },
            "species": {
              "Homo sapiens": 2,
              "Unknown": 1
            }
          }
        }
      ]
    },
    {
      "position": 2,
      "low_support": true,
      "entropy": 0.0,
      "support": 3,
      "distinct_variants_count": 0,
      "distinct_variants_incidence": 0.0,
      "variants": [
        {
          "sequence": "SASKEIKSF",
          "count": 3,
          "incidence": 100.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": {
            "species": {
              "Homo sapiens": 2,
              "Unknown": 1
            },
            "accession": {
              "AYD75325.1": 1,
              "QEP52131.1": 1,
              "AYD75365.1": 1
            },
            "strain": {
              "Sierra Leone": 3
            },
            "date": {
              "1979": 1,
              "2012": 1,
              "1980": 1
            }
          }
        }
      ]
    },
    {
      "position": 3,
      "low_support": true,
      "entropy": 0.0,
      "support": 3,
      "distinct_variants_count": 0,
      "distinct_variants_incidence": 0.0,
      "variants": [
        {
          "sequence": "ASKEIKSFL",
          "count": 3,
          "incidence": 100.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": {
            "strain": {
              "Sierra Leone": 3
            },
            "date": {
              "1980": 1,
              "2012": 1,
              "1979": 1
            },
            "species": {
              "Homo sapiens": 2,
              "Unknown": 1
            },
            "accession": {
              "AYD75365.1": 1,
              "QEP52131.1": 1,
              "AYD75325.1": 1
            }
          }
        }
      ]
    },
    {
      "position": 4,
      "low_support": true,
      "entropy": 0.0,
      "support": 3,
      "distinct_variants_count": 0,
      "distinct_variants_incidence": 0.0,
      "variants": [
        {
          "sequence": "SKEIKSFLW",
          "count": 3,
          "incidence": 100.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": {
            "accession": {
              "AYD75365.1": 1,
              "QEP52131.1": 1,
              "AYD75325.1": 1
            },
            "date": {
              "2012": 1,
              "1980": 1,
              "1979": 1
            },
            "strain": {
              "Sierra Leone": 3
            },
            "species": {
              "Homo sapiens": 2,
              "Unknown": 1
            }
          }
        }
      ]
    },
    {
      "position": 5,
      "low_support": true,
      "entropy": 0.0,
      "support": 3,
      "distinct_variants_count": 0,
      "distinct_variants_incidence": 0.0,
      "variants": [
        {
          "sequence": "KEIKSFLWT",
          "count": 3,
          "incidence": 100.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": {
            "date": {
              "1979": 1,
              "1980": 1,
              "2012": 1
            },
            "strain": {
              "Sierra Leone": 3
            },
            "accession": {
              "AYD75365.1": 1,
              "QEP52131.1": 1,
              "AYD75325.1": 1
            },
            "species": {
              "Unknown": 1,
              "Homo sapiens": 2
            }
          }
        }
      ]
    },
    {
      "position": 6,
      "low_support": true,
      "entropy": 0.0,
      "support": 3,
      "distinct_variants_count": 0,
      "distinct_variants_incidence": 0.0,
      "variants": [
        {
          "sequence": "EIKSFLWTQ",
          "count": 3,
          "incidence": 100.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": {
            "accession": {
              "QEP52131.1": 1,
              "AYD75365.1": 1,
              "AYD75325.1": 1
            },
            "species": {
              "Unknown": 1,
              "Homo sapiens": 2
            },
            "strain": {
              "Sierra Leone": 3
            },
            "date": {
              "1980": 1,
              "2012": 1,
              "1979": 1
            }
          }
        }
      ]
    },
    {
      "position": 7,
      "low_support": true,
      "entropy": 0.0,
      "support": 3,
      "distinct_variants_count": 0,
      "distinct_variants_incidence": 0.0,
      "variants": [
        {
          "sequence": "IKSFLWTQS",
          "count": 3,
          "incidence": 100.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": {
            "date": {
              "2012": 1,
              "1979": 1,
              "1980": 1
            },
            "species": {
              "Homo sapiens": 2,
              "Unknown": 1
            },
            "accession": {
              "QEP52131.1": 1,
              "AYD75325.1": 1,
              "AYD75365.1": 1
            },
            "strain": {
              "Sierra Leone": 3
            }
          }
        }
      ]
    },
    {
      "position": 8,
      "low_support": true,
      "entropy": 0.0,
      "support": 3,
      "distinct_variants_count": 0,
      "distinct_variants_incidence": 0.0,
      "variants": [
        {
          "sequence": "KSFLWTQSL",
          "count": 3,
          "incidence": 100.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": {
            "species": {
              "Homo sapiens": 2,
              "Unknown": 1
            },
            "accession": {
              "AYD75365.1": 1,
              "QEP52131.1": 1,
              "AYD75325.1": 1
            },
            "date": {
              "2012": 1,
              "1979": 1,
              "1980": 1
            },
            "strain": {
              "Sierra Leone": 3
            }
          }
        }
      ]
    },
    {
      "position": 9,
      "low_support": true,
      "entropy": 0.0,
      "support": 3,
      "distinct_variants_count": 0,
      "distinct_variants_incidence": 0.0,
      "variants": [
        {
          "sequence": "SFLWTQSLR",
          "count": 3,
          "incidence": 100.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": {
            "accession": {
              "QEP52131.1": 1,
              "AYD75325.1": 1,
              "AYD75365.1": 1
            },
            "species": {
              "Homo sapiens": 2,
              "Unknown": 1
            },
            "date": {
              "1979": 1,
              "1980": 1,
              "2012": 1
            },
            "strain": {
              "Sierra Leone": 3
            }
          }
        }
      ]
    },
    {
      "position": 10,
      "low_support": true,
      "entropy": 0.0,
      "support": 3,
      "distinct_variants_count": 0,
      "distinct_variants_incidence": 0.0,
      "variants": [
        {
          "sequence": "FLWTQSLRR",
          "count": 3,
          "incidence": 100.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": {
            "strain": {
              "Sierra Leone": 3
            },
            "species": {
              "Homo sapiens": 2,
              "Unknown": 1
            },
            "accession": {
              "AYD75325.1": 1,
              "QEP52131.1": 1,
              "AYD75365.1": 1
            },
            "date": {
              "1979": 1,
              "2012": 1,
              "1980": 1
            }
          }
        }
      ]
    },
    {
      "position": 11,
      "low_support": true,
      "entropy": 0.0,
      "support": 3,
      "distinct_variants_count": 0,
      "distinct_variants_incidence": 0.0,
      "variants": [
        {
          "sequence": "LWTQSLRRE",
          "count": 3,
          "incidence": 100.0,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": {
            "species": {
              "Homo sapiens": 2,
              "Unknown": 1
            },
            "strain": {
              "Sierra Leone": 3
            },
            "date": {
              "1980": 1,
              "2012": 1,
              "1979": 1
            },
            "accession": {
              "QEP52131.1": 1,
              "AYD75325.1": 1,
              "AYD75365.1": 1
            }
          }
        }
      ]
    },
    {
      "position": 12,
      "low_support": true,
      "entropy": 0.914294702419047,
      "support": 3,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 33.333336,
      "variants": [
        {
          "sequence": "WTQSLRREL",
          "count": 2,
          "incidence": 66.66667,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": {
            "accession": {
              "AYD75325.1": 1,
              "QEP52131.1": 1
            },
            "date": {
              "1979": 1,
              "2012": 1
            },
            "strain": {
              "Sierra Leone": 2
            },
            "species": {
              "Homo sapiens": 1,
              "Unknown": 1
            }
          }
        },
        {
          "sequence": "WTQSLRRES",
          "count": 1,
          "incidence": 33.333336,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "accession": {
              "AYD75365.1": 1
            },
            "date": {
              "1980": 1
            },
            "strain": {
              "Sierra Leone": 1
            },
            "species": {
              "Homo sapiens": 1
            }
          }
        }
      ]
    },
    {
      "position": 13,
      "low_support": true,
      "entropy": 0.9286973563836846,
      "support": 3,
      "distinct_variants_count": 1,
      "distinct_variants_incidence": 33.333336,
      "variants": [
        {
          "sequence": "TQSLRRELS",
          "count": 2,
          "incidence": 66.66667,
          "motif_short": "I",
          "motif_long": "Index",
          "metadata": {
            "date": {
              "2012": 1,
              "1979": 1
            },
            "strain": {
              "Sierra Leone": 2
            },
            "species": {
              "Homo sapiens": 1,
              "Unknown": 1
            },
            "accession": {
              "QEP52131.1": 1,
              "AYD75325.1": 1
            }
          }
        },
        {
          "sequence": "TQSLRRESS",
          "count": 1,
          "incidence": 33.333336,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "strain": {
              "Sierra Leone": 1
            },
            "species": {
              "Homo sapiens": 1
            },
            "date": {
              "1980": 1
            },
            "accession": {
              "AYD75365.1": 1
            }
          }
        }
      ]
    },
    {
      "position": 14,
      "low_support": true,
      "entropy": 1.590726304378389,
      "support": 3,
      "distinct_variants_count": 3,
      "distinct_variants_incidence": 100.0,
      "variants": [
        {
          "sequence": "QSLRRESSG",
          "count": 1,
          "incidence": 33.333336,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "strain": {
              "Sierra Leone": 1
            },
            "date": {
              "1980": 1
            },
            "accession": {
              "AYD75365.1": 1
            },
            "species": {
              "Homo sapiens": 1
            }
          }
        },
        {
          "sequence": "QSLRRELSS",
          "count": 1,
          "incidence": 33.333336,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "accession": {
              "QEP52131.1": 1
            },
            "strain": {
              "Sierra Leone": 1
            },
            "species": {
              "Homo sapiens": 1
            },
            "date": {
              "2012": 1
            }
          }
        },
        {
          "sequence": "QSLRRELSG",
          "count": 1,
          "incidence": 33.333336,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "strain": {
              "Sierra Leone": 1
            },
            "species": {
              "Unknown": 1
            },
            "accession": {
              "AYD75325.1": 1
            },
            "date": {
              "1979": 1
            }
          }
        }
      ]
    },
    {
      "position": 15,
      "low_support": true,
      "entropy": 1.5836823969940967,
      "support": 3,
      "distinct_variants_count": 3,
      "distinct_variants_incidence": 100.0,
      "variants": [
        {
          "sequence": "SLRRESSGY",
          "count": 1,
          "incidence": 33.333336,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "accession": {
              "AYD75365.1": 1
            },
            "species": {
              "Homo sapiens": 1
            },
            "strain": {
              "Sierra Leone": 1
            },
            "date": {
              "1980": 1
            }
          }
        },
        {
          "sequence": "SLRRELSGY",
          "count": 1,
          "incidence": 33.333336,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "accession": {
              "AYD75325.1": 1
            },
            "species": {
              "Unknown": 1
            },
            "date": {
              "1979": 1
            },
            "strain": {
              "Sierra Leone": 1
            }
          }
        },
        {
          "sequence": "SLRRELSSY",
          "count": 1,
          "incidence": 33.333336,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "strain": {
              "Sierra Leone": 1
            },
            "accession": {
              "QEP52131.1": 1
            },
            "species": {
              "Homo sapiens": 1
            },
            "date": {
              "2012": 1
            }
          }
        }
      ]
    },
    {
      "position": 16,
      "low_support": true,
      "entropy": 1.5880632175312825,
      "support": 3,
      "distinct_variants_count": 3,
      "distinct_variants_incidence": 100.0,
      "variants": [
        {
          "sequence": "LRRESSGYC",
          "count": 1,
          "incidence": 33.333336,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "accession": {
              "AYD75365.1": 1
            },
            "strain": {
              "Sierra Leone": 1
            },
            "species": {
              "Homo sapiens": 1
            },
            "date": {
              "1980": 1
            }
          }
        },
        {
          "sequence": "LRRELSSYC",
          "count": 1,
          "incidence": 33.333336,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "accession": {
              "QEP52131.1": 1
            },
            "strain": {
              "Sierra Leone": 1
            },
            "species": {
              "Homo sapiens": 1
            },
            "date": {
              "2012": 1
            }
          }
        },
        {
          "sequence": "LRRELSGYC",
          "count": 1,
          "incidence": 33.333336,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "strain": {
              "Sierra Leone": 1
            },
            "date": {
              "1979": 1
            },
            "accession": {
              "AYD75325.1": 1
            },
            "species": {
              "Unknown": 1
            }
          }
        }
      ]
    },
    {
      "position": 17,
      "low_support": true,
      "entropy": 1.5839045388565696,
      "support": 3,
      "distinct_variants_count": 3,
      "distinct_variants_incidence": 100.0,
      "variants": [
        {
          "sequence": "RRELSSYCS",
          "count": 1,
          "incidence": 33.333336,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "species": {
              "Homo sapiens": 1
            },
            "date": {
              "2012": 1
            },
            "accession": {
              "QEP52131.1": 1
            },
            "strain": {
              "Sierra Leone": 1
            }
          }
        },
        {
          "sequence": "RRELSGYCS",
          "count": 1,
          "incidence": 33.333336,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "accession": {
              "AYD75325.1": 1
            },
            "species": {
              "Unknown": 1
            },
            "strain": {
              "Sierra Leone": 1
            },
            "date": {
              "1979": 1
            }
          }
        },
        {
          "sequence": "RRESSGYCS",
          "count": 1,
          "incidence": 33.333336,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "species": {
              "Homo sapiens": 1
            },
            "strain": {
              "Sierra Leone": 1
            },
            "date": {
              "1980": 1
            },
            "accession": {
              "AYD75365.1": 1
            }
          }
        }
      ]
    },
    {
      "position": 18,
      "low_support": true,
      "entropy": 1.5856788550025385,
      "support": 3,
      "distinct_variants_count": 3,
      "distinct_variants_incidence": 100.0,
      "variants": [
        {
          "sequence": "RELSGYCSN",
          "count": 1,
          "incidence": 33.333336,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "accession": {
              "AYD75325.1": 1
            },
            "strain": {
              "Sierra Leone": 1
            },
            "species": {
              "Unknown": 1
            },
            "date": {
              "1979": 1
            }
          }
        },
        {
          "sequence": "RESSGYCSN",
          "count": 1,
          "incidence": 33.333336,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "accession": {
              "AYD75365.1": 1
            },
            "strain": {
              "Sierra Leone": 1
            },
            "date": {
              "1980": 1
            },
            "species": {
              "Homo sapiens": 1
            }
          }
        },
        {
          "sequence": "RELSSYCSN",
          "count": 1,
          "incidence": 33.333336,
          "motif_short": "U",
          "motif_long": "Unique",
          "metadata": {
            "date": {
              "2012": 1
            },
            "strain": {
              "Sierra Leone": 1
            },
            "accession": {
              "QEP52131.1": 1
            },
            "species": {
              "Homo sapiens": 1
            }
          }
        }
      ]
    }
  ]
}

Command-Line Arguments

Argument	Type	Required	Default	Example	Description
-h	N/A	False	N/A	dima-cli -h	Prints a summary of all available command-line arguments.
-n	String	False	Unknown	dima-cli -i sequences.afa -f "accession|strain|country" -n "NA"	Silently fix missing values in the FASTA header with given value.
-v	N/A	False	N/A	dima-cli -v	Prints the version of dima-cli that is currently installed.
-p	String	False	Unknown Protein	dima-cli -n "Coronavirus Surface Protein" -i sequences.afa	The name of the protein that will appear on the results.
-i	String	True	N/A	dima-cli -i sequences.afa	The path to the FASTA Multiple Sequence Alignment file.
-o	String	False	stdout (prints the results)	dima-cli -i sequences.afa -o results,json	The location where the results shall be saved.
-l	Integer	False	9	dima-cli -i sequences.afa -l 12	The length of the kmers generated.
-f	String	False	N/A	dima-cli -i sequences.afa -f "accession|strain|country"	The format of the FASTA header. Labels where each variant of a kmer position originated from.
-s	Integer	False	30	dima-cli -i sequences.afa -l 12 -s 40	The minimum required support for each kmer position.

Module Parameters

Parameter	Type	Required	Default	Description
sequences	String/StringIO	True	N/A	The path to a FASTA Multiple Sequence Alignment file (MSA), or a StringIO object containing FASTA MSA.
kmer_length	Integer	False	9	The length of the kmers generated.
header_fillna	String	False	Unknown	Silently fix missing values in the FASTA header with given value (only required when header_format is given).
json	Boolean	False	False	Whether the result is a JSON string, or a Python object.
header_format	String	False	N/A	The format of the FASTA header. Labels where each variant of a kmer position originated from.
support_threshold	Integer	False	30	The minimum required support for each kmer position.
protein_name	String	False	Unknown Protein	The name of the protein that will appear on the results.
json_save_path	String	False	stdout (prints to console)	The location where the results shall be saved (only required when json = True).