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

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.

$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


Guanliang MENG

6 Citation

Currently I have no plan to publish cigar_coordinates.

Project details

Uploaded source