从深度文件中提取序列深度。
depth-stat的Python项目详细描述
深度统计
1简介
depth_stat是一个从深度文件中提取序列深度并进行一些统计的工具。
见https://github.com/linzhi2013/depth_stat。
2安装
pip install depth_stat
将在与您的pip命令相同的目录下创建命令depth_stat。
3用法
3.1命令行
$ depth_stat
usage: depth_stat [-h] -i <file> [-q <str>] [-a <int>] [-b <int>]
[-f <file>]
To extract the sequence depth from depthfile.
The depthfile content format:
seqid1 depth1 depth2 depth3 ...
seqid2 depth1 depth2 depth3 ...
This script is part of the MitoZ project, by Guanliang MENG.
See https://github.com/linzhi2013/depth_stat.
optional arguments:
-h, --help show this help message and exit
-i <file> input depthfile
-q <str> sequence id
-a <int> the start position, Python-style (0-leftmost)
-b <int> the end position, Python-style for slicing
-f <file> a file of 'seqid start end' list on each line
3.2在python3脚本中
In [1]: from depth_stat import SeqDepth
In [2]: sdj = SeqDepth('DRR095708_mitoscaf.fa.fsa.depth')
In [3]: sdj.extract_range_depth(seqid='scaffold44450', start=0, end=20)
Out[3]: [1, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 6, 7, 7, 8, 8, 8, 8, 8, 8]
In [4]: sdj.range_depth_stat(seqid='scaffold44450', start=0, end=20)
Out[4]: ('scaffold44450', 0, 20, 1, 5.15, 8)
In [5]: sdj.range_depth_freq(seqid='scaffold44450', start=0, end=20)
Out[5]: [(1, 4), (4, 4), (5, 3), (6, 1), (7, 2), (8, 6)]
作者
孟冠良
引文
此脚本是软件包的一部分，当您在工作中使用此脚本时，请引用：
MitoZ: A toolkit for mitochondrial genome assembly, annotation and visualization with NGS data. Guangliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu (in manuscript)
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