Description:
depthstat 0.0.1
depth_stat
1 Introduction
depth_stat is a tool to extract the sequence depth from depthfile and do some statstics.
see https://github.com/linzhi2013/depth_stat.
2 Installation
pip install depth_stat
There will be a command depth_stat created under the same directory as your pip command.
3 Usage
3.1 command line
$ 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 in a Python3 script
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)]
Author
Guanliang MENG
Citation
This script is part of the package MitoZ, when you use the script in your work, please cite:
MitoZ: A toolkit for mitochondrial genome assembly, annotation and visualization with NGS data. Guangliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu (in manuscript)
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
Files:
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