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.

However, if you use this program in your analysis, or you "steal" the idea/codes of this program into your script, I should be one of the co-authors in your publication!!!