Description:

cigarcoordinates 0.0.1

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.

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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