To get the coordinates of a given CIGAR string. By Guanliang MENG, see https://github.com/linzhi2013/cigar_coordinates.
Project 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
.
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