https://github.com/waterflow80/genome-distance
Efficient way of calculating the distance between two genome sequences using the Jaccard Distance
https://github.com/waterflow80/genome-distance
Last synced: 3 months ago
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Efficient way of calculating the distance between two genome sequences using the Jaccard Distance
- Host: GitHub
- URL: https://github.com/waterflow80/genome-distance
- Owner: waterflow80
- Created: 2024-12-02T13:21:14.000Z (7 months ago)
- Default Branch: main
- Last Pushed: 2024-12-08T18:58:03.000Z (6 months ago)
- Last Synced: 2025-02-08T17:44:35.663Z (4 months ago)
- Language: Python
- Size: 2.27 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# genome-distance
Efficient way of calculating the distance between two genome sequences using the Jaccard Distance
## Run
To the run the code, follow the below steps:
```sh
git clone https://github.com/waterflow80/genome-distance.git
cd genome-distance
python3.11 -m venv venv
./venv/bin/activate
pip install -r requirements
python3.11 genome_distance.py
# You might need to include the python interpreter of the venv
# ./venv/bin/python3 genome_distance.py
```
When succefully executed, you should see something similar to the following:
```sh
Distance between NZ_AKBW01000001.1 and .14412_3_82.9 is: 0.9994697773064687
Distance between NZ_AKBW01000001.1 and .14412_3_82.10 is: 0.9994666666666666
Distance between NZ_AKBW01000001.1 and .14412_3_82.11 is: 1.0
Distance between NZ_AKBW01000001.1 and .14412_3_82.12 is: 0.9994706193753309
Distance between NZ_AKBW01000001.1 and .14412_3_82.13 is: 1.0
Distance between NZ_AKBW01000001.1 and AE007317.1 is: 0.26956521739130435
Distance between .14412_3_84.1 and .14412_3_84.2 is: 0.993798449612403
Distance between .14412_3_84.1 and .14412_3_84.3 is: 0.9943298969072165
Distance between .14412_3_84.1 and .14412_3_84.4 is: 0.994335736354274
Distance between .14412_3_84.1 and .14412_3_84.5 is: 0.9948293691830403
Distance between .14412_3_84.1 and .14412_3_84.6 is: 0.9974437627811861
Distance between .14412_3_84.1 and .14412_3_84.7 is: 0.9974385245901639
Distance between .14412_3_84.1 and .14412_3_84.8 is: 0.9969056214543579
Distance between .14412_3_84.1 and .14412_3_84.9 is: 0.9989801121876594
...
```
## Effect of Sketch Size
### Effect on distance
We tried to analyse the effect of the sketch size on the calcualted distance. So, we took two random sequences `.14412_3_84.17` and `.14412_3_82.13` and calulcated their distances using different values of the sketch size, and we got the following results:
We can see that for sketch sizes less than **1000**, the distance was unpredictable. But starting from **1000**, the distance remains the same at `0.08561643835616439`.
### Effect on calulation time
The following line plot illustrates the effect of the sketch size on execution time:
