Metadata-Version: 2.1
Name: depth-stat
Version: 0.0.1
Summary: To extract the sequence depth from depthfile.
Home-page: https://github.com/linzhi2013
Author: Guanliang Meng
Author-email: mengguanliang@foxmail.com
License: UNKNOWN
Description: # 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)
        
        
        
        
        
        
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Requires-Python: >=3
Description-Content-Type: text/markdown
