Metadata-Version: 2.1
Name: cigar-coordinates
Version: 0.0.1
Summary: To get the coordinates of a given CIGAR string. By Guanliang MENG, see https://github.com/linzhi2013/cigar_coordinates.
Home-page: https://github.com/linzhi2013/cigar_coordinates
Author: Guanliang Meng
Author-email: mengguanliang@foxmail.com
License: UNKNOWN
Description: # cigar_coordinates
        
        ## 1 Introduction
        
        `cigar_coordinates` is a tool To get the coordinates of a given CIGAR string. CIGARs are in respect of the reference sequence. By Guanliang MENG, see https://github.com/linzhi2013/cigar_coordinates. 
        
        `cigar_coordinates` understands the following CIGAR characters:
        
               seq - - - N N N O O O
            refseq - N O N - O O N -
             cigar P n D B u U M N I
        
        
        ## 2 Installation
        
            pip install cigar_coordinates
        
        There will be a command `cigar_coordinates` created under the same directory as your `pip` command.
        
        ## 3 Usage
            
            $ cigar_coordinates
            usage: cigar_coordinates [-h] -c <STR> [-s <INT>] [-q] [-d {+,-}]
        
            To get the coordinates of a given CIGAR string.
            By Guanliang MENG, see https://github.com/linzhi2013/cigar_coordinates.
        
            I understand the following CIGAR types:
        
                 seq - - - N N N O O O
              refseq - N O N - O O N -
               cigar P n D B u U M N I
        
            The output coordinates are closed intervals.
        
            optional arguments:
              -h, --help  show this help message and exit
              -c <STR>    input CIGAR string
              -s <INT>    the start coordinate on the sequence, whatever the gene
                          direction is, this option is always the smaller one. [1]
              -q          the '-s' option is about query sequence, not refseq [True]
              -d {+,-}    the gene direction [+]
        
        ## 4 Example
          
        For a gene: ND1;len=945;\[2444:3389\]\(\+\)
        
            $ cigar_coordinates -c 6D166M268N511M -s 2444
            6D  2444  2444
            166M  2444  2609
            268N  2610  2877
            511M  2878  3388
        
        ## 5 Author
        Guanliang MENG
        
        ## 6 Citation
        Currently I have no plan to publish `cigar_coordinates`.
        
        
        
        
        
        
        
        
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
