msa_cigars is a tool to get the CIGARs of a multiple sequence alignment. ONE alignment in the input file is assumed! CIGARs are in respect of the reference sequence. By Guanliang MENG, see https://github.com/linzhi2013/msa_cigars.
pip install msa_cigars
There will be a command msa_cigars created under the same directory as your pip command.
$ msa_cigars
usage: msa_cigars [-h] -i <FILE> -refseq_id <STR> [-n <STR>] [-g <STR>]
[-f <FORMAT>] [-o <FILE>]
To get the CIGARs of a multiple sequence alignment.
ONE alignment in the input file is assumed!
CIGARs are in respect of the reference sequence.
'O' normal bases, e.g. A, T, G, C
'-' deletion
'N' unknown base
seq - - - N N N O O O
refseq - N O N - O O N -
cigar P n D B u U M N I
By Guanliang MENG,
see https://github.com/linzhi2013/msa_cigars.
optional arguments:
-h, --help show this help message and exit
-i <FILE> input msa file
-refseq_id <STR> MsaCigars class uses regular expression to find out the
sequence id of refseq. Thus, make sure the value of
'refseq_id' option is unique among the input msa file.
-n <STR> character of unknown base [N]
-g <STR> character of gap base [-]
-f <FORMAT> the msa format [fasta]
-o <FILE> outfile name [stdout]
Guanliang MENG
Currently I have no plan to publish msa_cigars. 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!!!
However, since msa_cigars makes use of Biopython, you should also cite it if you use breakSeqInNs_then_translate in your work:
Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, Michiel J. L. de Hoon: “Biopython: freely available Python tools for computational molecular biology and bioinformatics”. Bioinformatics 25 (11), 1422–1423 (2009). https://doi.org/10.1093/bioinformatics/btp163
Please go to http://www.biopython.org/ for more details.