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

Project description

DiMA - Diversity Motif Analyser

Table of Contents

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

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", sequences_source='file').run()

Results

{
   "sequence_count":203,
   "support_threshold":30,
   "low_support":false,
   "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", sequences_source='file', header_format="accession|strain|country|date").run()

Results

{
   "sequence_count":203,
   "support_threshold":30,
   "low_support":false,
   "protein_name":"Unknown Protein",
   "kmer_length":9,
   "results":[
      {
         "position":1,
         "low_support":false,
         "entropy":0.8361476856397749,
         "support":124,
         "distinct_variants_count":4,
         "distinct_variants_incidence":3.2258062,
         "variants":[
            {
               "sequence":"MKNIIALSY",
               "count":13,
               "incidence":10.4838705,
               "motif_short":"Ma",
               "motif_long":"Major",
               "metadata":{
                  "strain":[
                     "A/India/Pun_1922030/2019",
                     "A/India/Pun_1922292/2019",
                     "A/India/Pun_1921693/2019",
                     "A/India/Pun_1922218/2019",
                     "A/India/Pun_1922278/2019",
                     "A/India/Pun_1924667/2019",
                     "A/India/Pun_1923708/2019",
                     "A/India/Pun_1921994/2019",
                     "A/India/Pun_1922260/2019",
                     "A/India/Pun_1922016/2019",
                     "A/India/Pun_1923690/2019",
                     "A/India/Pun_1922295/2019",
                     "A/India/Pun_1923665/2019"
                  ],
                  "country":[
                     "India",
                     "India",
                     "India",
                     "India",
                     "India",
                     "India",
                     "India",
                     "India",
                     "India",
                     "India",
                     "India",
                     "India",
                     "India"
                  ],
                  "accession":[
                     "MN955496",
                     "MN955492",
                     "MN955499",
                     "MN955502",
                     "MN955493",
                     "MN955488",
                     "MN955487",
                     "MN955498",
                     "MN955494",
                     "MN955497",
                     "MN955489",
                     "MN955491",
                     "MN955490"
                  ],
                  "date":[
                     "08/04/2019",
                     "08/19/2019",
                     "07/17/2019",
                     "08/09/2019",
                     "08/18/2019",
                     "08/01/2019",
                     "09/07/2019",
                     "07/26/2019",
                     "08/16/2019",
                     "07/30/2019",
                     "08/31/2019",
                     "08/20/2019",
                     "09/01/2019"
                  ]
               }
            },
            {
               "sequence":"MKTIIALSY",
               "count":105,
               "incidence":84.67742,
               "motif_short":"I",
               "motif_long":"Index",
               "metadata":{
                  "date":[
                     "01/02/2019",
                     "02/17/2019",
                     "01/14/2019",
                     "02/17/2019",
                     "01/17/2019",
                     "03/14/2019",
                     "02/13/2019",
                     "01/02/2019",
                     "02/06/2019",
                     "01/18/2019",
                     "10/11/2019",
                     "11/15/2019",
                     "01/10/2019",
                     "01/17/2019",
                     "01/17/2019",
                     "01/24/2019",
                     "02/01/2019",
                     "02/01/2019",
                     "02/01/2019",
                     "02/14/2019",
                     "03/14/2019",
                     "07/25/2019",
                     "08/21/2019",
                     "09/05/2019",
                     "09/05/2019",
                     "03/2019",
                     "02/2019",
                     "01/28/2019",
                     "10/08/2019",
                     "03/27/2019",
                     "02/14/2019",
                     "03/14/2019",
                     "01/15/2019",
                     "01/19/2019",
                     "01/28/2019",
                     "01/18/2019",
                     "02/14/2019",
                     "01/04/2019",
                     "01/08/2019",
                     "01/07/2019",
                     "01/28/2019",
                     "01/2019",
                     "01/10/2019",
                     "01/11/2019",
                     "01/13/2019",
                     "01/24/2019",
                     "01/08/2019",
                     "01/09/2019",
                     "01/14/2019",
                     "01/10/2019",
                     "02/2019",
                     "01/2019",
                     "09/05/2019",
                     "01/19/2019",
                     "01/03/2019",
                     "01/23/2019",
                     "02/01/2019",
                     "02/21/2019",
                     "02/28/2019",
                     "02/05/2019",
                     "01/07/2019",
                     "01/08/2019",
                     "01/08/2019",
                     "01/28/2019",
                     "01/28/2019",
                     "01/29/2019",
                     "01/29/2019",
                     "01/29/2019",
                     "01/30/2019",
                     "01/30/2019",
                     "01/30/2019",
                     "01/31/2019",
                     "01/31/2019",
                     "01/31/2019",
                     "01/09/2019",
                     "02/27/2019",
                     "03/05/2019",
                     "03/05/2019",
                     "03/05/2019",
                     "03/05/2019",
                     "03/08/2019",
                     "03/08/2019",
                     "03/04/2019",
                     "03/12/2019",
                     "01/05/2019",
                     "01/28/2019",
                     "01/29/2019",
                     "01/31/2019",
                     "02/22/2019",
                     "03/05/2019",
                     "01/23/2019",
                     "02/19/2019",
                     "04/14/2019",
                     "01/17/2019",
                     "04/04/2019",
                     "02/01/2019",
                     "02/01/2019",
                     "03/21/2019",
                     "05/24/2019",
                     "08/13/2019",
                     "08/05/2019",
                     "01/08/2019",
                     "01/14/2019",
                     "01/21/2019",
                     "01/12/2019"
                  ],
                  "country":[
                     "Iran",
                     "Iran",
                     "Turkey",
                     "Iran",
                     "China",
                     "China",
                     "India",
                     "Iran",
                     "India",
                     "Japan",
                     "China",
                     "China",
                     "China",
                     "China",
                     "China",
                     "China",
                     "China",
                     "China",
                     "China",
                     "China",
                     "China",
                     "China",
                     "China",
                     "China",
                     "China",
                     "China",
                     "China",
                     "Japan",
                     "China",
                     "Japan",
                     "China",
                     "China",
                     "Japan",
                     "Japan",
                     "Japan",
                     "South_Korea",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "China",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "South_Korea",
                     "South_Korea",
                     "South_Korea",
                     "South_Korea",
                     "China",
                     "China",
                     "China",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "South_Korea",
                     "South_Korea",
                     "South_Korea",
                     "South_Korea",
                     "South_Korea",
                     "South_Korea",
                     "South_Korea",
                     "South_Korea",
                     "South_Korea",
                     "South_Korea",
                     "Japan",
                     "Japan",
                     "Japan",
                     "Japan",
                     "South_Korea",
                     "South_Korea",
                     "Japan",
                     "South_Korea",
                     "South_Korea",
                     "Japan",
                     "South_Korea",
                     "China",
                     "China",
                     "China",
                     "India",
                     "India",
                     "India",
                     "South_Korea",
                     "South_Korea",
                     "South_Korea",
                     "South_Korea"
                  ],
                  "accession":[
                     "MK592790",
                     "MK648247",
                     "MK840323",
                     "MK648248",
                     "MT102500",
                     "MT102510",
                     "MK592841",
                     "MK592791",
                     "MK592842",
                     "MK785815",
                     "MT102520",
                     "MT102521",
                     "MT102498",
                     "MT102499",
                     "MT102501",
                     "MT102502",
                     "MT102504",
                     "MT102506",
                     "MT102507",
                     "MT102508",
                     "MT102512",
                     "MT102514",
                     "MT102515",
                     "MT102516",
                     "MT102517",
                     "MN594842",
                     "MN594840",
                     "MK869211",
                     "MT102519",
                     "MN074410",
                     "MT102509",
                     "MT102511",
                     "MK785807",
                     "MK785831",
                     "MK633673",
                     "MK763864",
                     "MN873980",
                     "MK905306",
                     "MK633641",
                     "MK576906",
                     "MK633649",
                     "MN594838",
                     "MK743434",
                     "MK743442",
                     "MK743450",
                     "MK785847",
                     "MK763014",
                     "MK786319",
                     "MK869555",
                     "MK869563",
                     "MN594841",
                     "MN594839",
                     "MT102518",
                     "MK785823",
                     "MK576890",
                     "MK785839",
                     "MK869203",
                     "MK912758",
                     "MK912766",
                     "MK927223",
                     "MK633617",
                     "MK633625",
                     "MK633633",
                     "MK633657",
                     "MK633681",
                     "MK633689",
                     "MK633697",
                     "MK898645",
                     "MK633705",
                     "MK633713",
                     "MK633721",
                     "MK633729",
                     "MK633737",
                     "MK898652",
                     "MK868723",
                     "MK913110",
                     "MK913126",
                     "MK913134",
                     "MK913142",
                     "MK913158",
                     "MK913166",
                     "MK913174",
                     "MK913182",
                     "MN169149",
                     "MK576898",
                     "MK633665",
                     "MK898639",
                     "MK898657",
                     "MK913102",
                     "MK913150",
                     "MK762978",
                     "MK913118",
                     "MN081410",
                     "MK742954",
                     "MN074010",
                     "MT102503",
                     "MT102505",
                     "MT102513",
                     "MN955500",
                     "MN955495",
                     "MN955501",
                     "MK763848",
                     "MK763856",
                     "MK763872",
                     "MK869539"
                  ],
                  "strain":[
                     "A/Alborz/153084/2019",
                     "A/Iran/Clinical_Sample/2019",
                     "A/Turkey/8543/2019",
                     "A/Iran/Clinical_Sample/2019",
                     "A/Homo_sapien/China/LS320/2019",
                     "A/Homo_sapien/China/LS330/2019",
                     "A/India/Pun_19615/2019",
                     "A/Alborz/153427/2019",
                     "A/India/Pun_19533/2019",
                     "A/Japan/8262/2019",
                     "A/Homo_sapien/China/LS340/2019",
                     "A/Homo_sapien/China/LS341/2019",
                     "A/Homo_sapien/China/LS318/2019",
                     "A/Homo_sapien/China/LS319/2019",
                     "A/Homo_sapien/China/LS321/2019",
                     "A/Homo_sapien/China/LS322/2019",
                     "A/Homo_sapien/China/LS324/2019",
                     "A/Homo_sapien/China/LS326/2019",
                     "A/Homo_sapien/China/LS327/2019",
                     "A/Homo_sapien/China/LS328/2019",
                     "A/Homo_sapien/China/LS332/2019",
                     "A/Homo_sapien/China/LS334/2019",
                     "A/Homo_sapien/China/LS335/2019",
                     "A/Homo_sapien/China/LS336/2019",
                     "A/Homo_sapien/China/LS337/2019",
                     "A/Wuhan/11193/2019",
                     "A/Wuhan/1120/2019",
                     "A/Japan/8604/2019",
                     "A/Homo_sapien/China/LS339/2019",
                     "A/Japan/9505/2019",
                     "A/Homo_sapien/China/LS329/2019",
                     "A/Homo_sapien/China/LS331/2019",
                     "A/Japan/8261/2019",
                     "A/Japan/8264/2019",
                     "A/Japan/NHRC_OID_FDX70576/2019",
                     "A/South_Korea/8207/2019",
                     "A/Yokosuka/NHRC_OID_FDX70622/2019",
                     "A/Japan/NHRC_OID_FDX70557/2019",
                     "A/Japan/NHRC_OID_FDX70566/2019",
                     "A/Japan/7848/2019",
                     "A/Japan/NHRC_OID_FDX70571/2019",
                     "A/Wuhan/345/2019",
                     "A/Japan/8000/2019",
                     "A/Japan/8001/2019",
                     "A/Japan/8002/2019",
                     "A/Japan/8266/2019",
                     "A/South_Korea/8203/2019",
                     "A/South_Korea/8352/2019",
                     "A/South_Korea/8671/2019",
                     "A/South_Korea/8674/2019",
                     "A/Wuhan/5413/2019",
                     "A/Wuhan/877/2019",
                     "A/Homo_sapien/China/LS338/2019",
                     "A/Japan/8263/2019",
                     "A/Japan/7846/2019",
                     "A/Japan/8265/2019",
                     "A/Japan/8603/2019",
                     "A/Japan/8768/2019",
                     "A/Japan/8769/2019",
                     "A/Japan/8957/2019",
                     "A/Japan/NHRC_OID_FDX70561/2019",
                     "A/Japan/NHRC_OID_FDX70563/2019",
                     "A/Japan/NHRC_OID_FDX70564/2019",
                     "A/Japan/NHRC_OID_FDX70572/2019",
                     "A/Japan/NHRC_OID_FDX70577/2019",
                     "A/Japan/NHRC_OID_FDX70579/2019",
                     "A/Japan/NHRC_OID_FDX70583/2019",
                     "A/Japan/NHRC_OID_FDX70584/2019",
                     "A/Japan/NHRC_OID_FDX70586/2019",
                     "A/Japan/NHRC_OID_FDX70587/2019",
                     "A/Japan/NHRC_OID_FDX70589/2019",
                     "A/Japan/NHRC_OID_FDX70590/2019",
                     "A/Japan/NHRC_OID_FDX70591/2019",
                     "A/Japan/NHRC_OID_FDX70592/2019",
                     "A/South_Korea/8667/2019",
                     "A/South_Korea/8823/2019",
                     "A/South_Korea/8825/2019",
                     "A/South_Korea/8826/2019",
                     "A/South_Korea/8827/2019",
                     "A/South_Korea/8829/2019",
                     "A/South_Korea/8830/2019",
                     "A/South_Korea/8831/2019",
                     "A/South_Korea/8832/2019",
                     "A/South_Korea/9116/2019",
                     "A/Japan/7847/2019",
                     "A/Japan/NHRC_OID_FDX70574/2019",
                     "A/Japan/NHRC_OID_FDX70581/2019",
                     "A/Japan/NHRC_OID_FDX70593/2019",
                     "A/South_Korea/8822/2019",
                     "A/South_Korea/8828/2019",
                     "A/Japan/8142/2019",
                     "A/South_Korea/8824/2019",
                     "A/South_Korea/9704/2019",
                     "A/Japan/8003/2019",
                     "A/South_Korea/9578/2019",
                     "A/Homo_sapien/China/LS323/2019",
                     "A/Homo_sapien/China/LS325/2019",
                     "A/Homo_sapien/China/LS333/2019",
                     "A/India/Pun_1920970/2019",
                     "A/India/Pun_1922253/2019",
                     "A/India/Pun_1922052/2019",
                     "A/South_Korea/8204/2019",
                     "A/South_Korea/8206/2019",
                     "A/South_Korea/8208/2019",
                     "A/South_Korea/8668/2019"
                  ]
               }
            },
            {
               "sequence":"MKTIIALSC",
               "count":2,
               "incidence":1.6129031,
               "motif_short":"Mi",
               "motif_long":"Minor",
               "metadata":{
                  "accession":[
                     "MN169648",
                     "MN873990"
                  ],
                  "country":[
                     "Japan",
                     "Japan"
                  ],
                  "strain":[
                     "A/Japan/9070/2019",
                     "A/Yokosuka/NHRC_OID_FDX70722/2019"
                  ],
                  "date":[
                     "03/12/2019",
                     "04/17/2019"
                  ]
               }
            },
            {
               "sequence":"METISLISM",
               "count":1,
               "incidence":0.80645156,
               "motif_short":"U",
               "motif_long":"Unique",
               "metadata":{
                  "accession":[
                     "MN853423"
                  ],
                  "country":[
                     "China"
                  ],
                  "strain":[
                     "A/Beijing/16/2019"
                  ],
                  "date":[
                     "01/2019"
                  ]
               }
            },
            {
               "sequence":"MKTIIALSH",
               "count":3,
               "incidence":2.4193547,
               "motif_short":"Mi",
               "motif_long":"Minor",
               "metadata":{
                  "country":[
                     "South_Korea",
                     "South_Korea",
                     "South_Korea"
                  ],
                  "date":[
                     "04/05/2019",
                     "04/10/2019",
                     "04/11/2019"
                  ],
                  "strain":[
                     "A/South_Korea/9579/2019",
                     "A/South_Korea/9645/2019",
                     "A/South_Korea/9646/2019"
                  ],
                  "accession":[
                     "MN074938",
                     "MN078683",
                     "MN078691"
                  ]
               }
            }
         ]
      }
   ]
}

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.
-v N/A False N/A dima-cli -v Prints the version of dima-cli that is currently installed.
-n 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 True N/A The path to a FASTA Multiple Sequence Alignment file (MSA), or a string containing FASTA MSA.
sequences_source String True N/A The source of the sequences (ie: "file" or "string")
kmer_length Integer False 9 The length of the kmers generated.
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 python json = True).

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