用于HI-C接触图的蛇形装箱包
serpentine的Python项目详细描述
蛇形装箱
局部涂抹hi-c接触图中的噪声区域，作为微分分析的前奏
目录
概要
将其用作Python3库：
importnumpyasnpimportserpentineasspA=np.loadtxt('./demos/A.csv')B=np.loadtxt('./demos/B.csv')trend,threshold=sp.MDbefore(A,B,show=False)sA,sB,sK=sp.serpentin_binning(A,B,threshold,threshold/5)
或者作为一个独立的unix工具：
$ serpentine --help
Serpentine binning
An implementation of the so-called 'serpentine binning' procedure described
in Scolari et al.
Command line::
Usage:
serpentine.py [<matrixA>] [<matrixB>] [--threshold=auto] [--verbose]
[--min-threshold=auto] [--trend=high] [--triangular]
[--limit=3] [--demo] [--demo-size=500]
Arguments:
matrixA The first input matrix, in plain text
CSV format. Optional in demo mode.
matrixB The second input matrix, in plain text
CSV format. Optional in demo mode or
single binning mode.
Options:
-h, --help Display this help message.
--version Display the program's current version.
-t auto, --threshold auto Threshold value to trigger binning.
[default: auto]
-m auto, --min-threshold auto Minimum value to force trigger binning
in either matrix. [default: auto]
--trend high Trend to subtract to the differential
matrix, possible values are "mean":
equal amount of positive and negative
differences, and "high": normalize
at the regions with higher coverage.
[default: high]
--triangular Treat the matrix as triangular,
useful when plotting matrices adjacent
to the diagonal. [default: False]
--limit 3 Set the z-axis limit on the
plot of the differential matrix.
[default: 3]
--demo Run a demo on randomly generated
matrices. [default: False]
--demo-size 500 Size of the test matrix for the demo.
[default: 500]
-v, --verbose Show verbose output. [default: False]
安装
sudo pip3 install -e git+https://github.com/koszullab/serpentine.git@master#egg=serpentine
文档
执行命令serpentine --help将提供命令行工具的简要帮助。有关python库函数的详细参考，请
阅读documentation。
作者
集群破坏者（scovit，a.k.a.vittore f.scolari）， lyamovich（baudrly，又名lyam baudry）
版权和许可
版权所有©2017巴斯德研究所，本软件开发于 巴斯德研究所染色体空间调控小组， 法国巴黎。
这个库是免费软件；您可以重新分发和/或修改它 在艺术许可下。
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