https://github.com/hexylena/gene2accession2kyotocabinet

Converts gene2accession file provided by NCBI into a fast kyoto-cabinet database
https://github.com/hexylena/gene2accession2kyotocabinet

Last synced: 16 days ago
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Converts gene2accession file provided by NCBI into a fast kyoto-cabinet database

• Host: GitHub
• URL: https://github.com/hexylena/gene2accession2kyotocabinet
• Owner: hexylena
• License: gpl-3.0
• Created: 2015-12-21T19:43:44.000Z (almost 9 years ago)
• Default Branch: master
• Last Pushed: 2015-12-21T19:46:21.000Z (almost 9 years ago)
• Last Synced: 2024-10-17T13:58:20.845Z (about 1 month ago)
• Language: Python
• Homepage:
• Size: 13.7 KB
• Stars: 2
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# gene2accession2kyotocabinet

This repository contains a simple makefile and python script for converting

NCBI's gene2accession table into an extremely fast kyotoCabinet database for

searching

## Examples

```console

$ make

# This step takes a long time. First it extracts the protein + genome GIs into

# the gene2accession.min.tsv file. Then they're converted into a kyoto-cabinet

# database (gene2accession.kch)

$ du -h gene2accession.*

845M    gene2accession.kch

517M    gene2accession.min.tsv

4.8G    gene2accession.tsv

# At the end, our database is lightning fast:

$ (env)user@host: time python lookup-test.py

  3282737 =>    3282736

 10954455 =>   10954454

  3282739 =>    3282736

 10954457 =>   10954454

  3282740 =>    3282736

219730360 =>  219730359

219783138 =>  219783137

257293830 =>  257293829

257287470 =>  257287469

 10954458 =>   10954454

  3282741 =>    3282736

real    0m0.015s

user    0m0.010s

sys     0m0.005s

```

## License

GPLv3