https://github.com/codecreatede/mongodb-genome

a mongodb implementation for pacbiohifi genome and genome annotation
https://github.com/codecreatede/mongodb-genome

bioinformatics database database-management database-schema genome-analysis genome-bioinformatics genome-informatics mongodb mongodb-database python3

Last synced: 4 days ago
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a mongodb implementation for pacbiohifi genome and genome annotation

• Host: GitHub
• URL: https://github.com/codecreatede/mongodb-genome
• Owner: codecreatede
• License: mit
• Created: 2024-08-17T18:19:45.000Z (about 2 months ago)
• Default Branch: main
• Last Pushed: 2024-09-12T09:14:30.000Z (21 days ago)
• Last Synced: 2024-09-26T01:35:14.300Z (7 days ago)
• Topics: bioinformatics, database, database-management, database-schema, genome-analysis, genome-bioinformatics, genome-informatics, mongodb, mongodb-database, python3
• Language: Python
• Homepage:
• Size: 131 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# mongodb-genome

- python class to prepare the genome files for the mongodb atlas

- since the genome annotations id will be same, implmented a list based nested iteration so that it can be inserted into ``` mongodb as .insertMany() ```

- below is the UML for the following class.



  

```

# if you are executing from the specific directory then

import os

os.chdir("path/dir/fasta/gff")

mongodbprepare("samplefile.gff", prepare= "yes")

fastaindex("samplefile.fasta", prepare= "yes")

exonparse("samplefile.gff", prepare= "yes")

intronparse("samplefile.gff", prepare= "yes")

exonseq("samplefile.gff", "samplefile.fasta", mongoexonprepareseq)

intronseq("samplefile.gff", "samplefile.fasta", mongointronprepareseq)

goparsemongo("GO_slim_sample.txt")

```

Gaurav Sablok