https://github.com/applicativesystem/domain-analyzer

domain analyzer for analyzing interpro domains
https://github.com/applicativesystem/domain-analyzer

bacterial-domains bacterial-genome-analysis bacterial-genomes bioinfromatics domain-analysis genome-analysis interpro

Last synced: 7 days ago
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domain analyzer for analyzing interpro domains

• Host: GitHub
• URL: https://github.com/applicativesystem/domain-analyzer
• Owner: applicativesystem
• License: mit
• Created: 2024-08-17T18:21:45.000Z (4 months ago)
• Default Branch: main
• Last Pushed: 2024-09-12T09:12:27.000Z (3 months ago)
• Last Synced: 2024-11-10T20:18:06.046Z (about 1 month ago)
• Topics: bacterial-domains, bacterial-genome-analysis, bacterial-genomes, bioinfromatics, domain-analysis, genome-analysis, interpro
• Language: Python
• Homepage:
• Size: 39.1 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# domain-analyzer

- This repository contains a datascience based faster implementation of the domain predictions from the interpro scan and it will give you a complete domains information, coordinates and other associative information. 

- I used a mapping dataframe approach to make it faster rather than looping it over and over. 

```python

bacterialProteomeDomainAnalyzer("/Users/gauravsablok/Desktop/CodeTest/json_parser/ipr_scan.json", \

                                                     arg_type = "getdomains")

[['G3DSA:3.30.70.20'],

 ['SSF53323', 'Pyruvate-ferredoxin oxidoreductase, PFOR, domain III'],

 ['G3DSA:3.40.50.920'],

 ['cd07034', 'TPP_PYR_PFOR_IOR-alpha_like', 'TPP_PYR_PFOR_IOR-alpha_like'],

 ['PIRSR005784-1', 'PIRSR005784-1'],

 ['PF01855',

  'POR_N',

  'Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg'],

 ['G3DSA:3.40.50.970:FF:000012',

  'Pyruvate:ferredoxin (Flavodoxin) oxidoreductase']]

help(bacterialProteomeDomainAnalyzer) # for more information

```

Gaurav Sablok \

University of Potsdam \

Potsdam,Germany