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)