TODO:添加peaksq描述
peaksql的Python项目详细描述
注意:此包正在进行开发,功能可能会更改或无法正常工作(尚未)!
峰值SQL
基因组学动态机器学习数据库。支持常见的类bed数据格式,如.bed和.narrowPeak。bedgraph;以及二进制bigwig格式。在
安装
PeakSQL可以通过pip安装:
pip install peaksql
或从源安装:
^{pr2}$入门
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:
...
- 项目
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