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https://github.com/andrewdalpino/dnahash
A specialized datastructure for counting short DNA sequences for use in Bioinformatics.
https://github.com/andrewdalpino/dnahash
bioinformatics k-mer-counting
Last synced: about 1 month ago
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A specialized datastructure for counting short DNA sequences for use in Bioinformatics.
- Host: GitHub
- URL: https://github.com/andrewdalpino/dnahash
- Owner: andrewdalpino
- License: mit
- Created: 2024-10-12T21:52:43.000Z (3 months ago)
- Default Branch: master
- Last Pushed: 2024-10-29T06:26:23.000Z (2 months ago)
- Last Synced: 2024-10-29T06:28:15.865Z (2 months ago)
- Topics: bioinformatics, k-mer-counting
- Language: Python
- Homepage:
- Size: 82 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# DNA Hash
A specialized datastructure and tokenization library for counting genetic sequences for use in Machine Learning and Bioinformatics. DNA Hash stores k-mer sequence counts by their up2bit encoding - an efficient two-way hash that works with variable-length sequences. As such, DNA Hash uses considerably less memory than a lookup table that stores sequences in plaintext. In addition, DNA Hash's novel autoscaling Bloom filter eliminates the need to explicitly store singletons and makes it suitable for use on streaming data.
- **Ultra-low** memory footprint
- **Variable** sequence lengths
- **Embarrassingly** parallelizable
- **Open-source** and free to use commercially
> **Note:** Due to the probabilistic nature of the Bloom filter, DNA Hash may over count sequences at a bounded rate.
## Installation
Install DNA Hash using a Python [package manager](https://packaging.python.org/en/latest/tutorials/installing-packages/), example pip:
```
pip install dnahash
```
## Example Usage
```python
from dna_hash import DNAHash
from dna_hash.tokenizers import Kmer, Canonical
from Bio import SeqIO
from matplotlib import pyplot as plt
hash_table = DNAHash(max_false_positive_rate=0.001)
tokenizer = Canonical(Kmer(6))
with open('covid-19-virus.fasta', 'r') as file:
for record in SeqIO.parse(file, 'fasta'):
for token in tokenizer.tokenize(str(record.seq)):
hash_table.increment(token)
for sequence, count in hash_table.top(25):
print(f'{sequence}: {count}')
print(f'Total sequences: {hash_table.num_sequences}')
print(f'# of unique sequences: {hash_table.num_unique_sequences}')
print(f'# of singletons: {hash_table.num_singletons}')
plt.hist(list(hash_table.counts.values()), bins=20)
plt.title('SARS-CoV-2 Genome')
plt.xlabel('Counts')
plt.ylabel('Frequency')
plt.show()
```
```
TAACAA: 70
TTAAAA: 68
ACAACA: 65
...
CATTAA: 49
Total sequences: 29876
# of unique sequences: 2013
# of singletons: 100
```
## References
- [1] https://github.com/JohnLonginotto/ACGTrie/blob/master/docs/UP2BIT.md.
- [2] P. Melsted et al. (2011). Efficient counting of k-mers in DNA sequences using a bloom filter.
- [3] S. Deorowicz et al. (2015). KMC 2: fast and resource-frugal k-mer counting.
- [4] A. DalPino. (2021). OkBloomer, a novel autoscaling Bloom Filter [[link](https://github.com/andrewdalpino/PyBloomer)].