To return CIGAR strings of a multiple sequences alignment
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
$ 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]
Currently I have no plan to publish
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.
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