Note: This package is in active development and functionality might change or not work correctly (yet)!
PeakSQL
Dynamic machine learning database for genomics. Supports common bed-like dataformats like .bed, and .narrowPeak. bedgraph; and the binary bigwig format.
Installation
PeakSQL can be installed through pip:
pip install peaksql
Or installed from source:
git clone https://github.com/vanheeringen-lab/peaksql
cd peaksql
pip install .
Getting started
import peaksql
# paths to our files
db_file = 'peakSQL.sqlite' # where to store our database
assembly = "/path/to/hg38.fa"
data = "binding_sites.bed"
# load data into database
db = peaksql.database.DataBase(db_file)
db.add_assembly(assembly, assembly="hg38", species="human")
db.add_data(data, assembly="data")
# now load as dataset
dataset = peaksql.BedRegionDataSet(db_file, seq_length=101, stride=200)
# use the dataset in your application
for seq, label in dataset:
...
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Metadata
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Release files for peaksql 0.0.4
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| peaksql-0.0.4.tar.gz | 14.1 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| peaksql-0.0.4-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 28.0 kB
Release files / peaksql-0.0.4.tar.gz
| Download URL | peaksql-0.0.4.tar.gz |
|---|---|
| Size | 14.1 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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No |
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twine/3.1.1 pkginfo/1.5.0.1 requests/2.23.0 setuptools/46.1.3 requests-toolbelt/0.9.1 tqdm/4.45.0 CPython/3.7.7
|
Release files / peaksql-0.0.4-py3-none-any.whl
| Download URL | peaksql-0.0.4-py3-none-any.whl |
|---|---|
| Size | 13.9 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
41dc76b5b6f1cf6868599897ffd4d4d2ec378bed1b5e3986ec9a4ec982bbfac4
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.1.1 pkginfo/1.5.0.1 requests/2.23.0 setuptools/46.1.3 requests-toolbelt/0.9.1 tqdm/4.45.0 CPython/3.7.7
|
