msa-cigars 0.0.1

To return CIGAR strings of a multiple sequences alignment

msa_cigars

1 Introduction

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.

2 Installation

pip install msa_cigars

There will be a command msa_cigars created under the same directory as your pip command.

3 Usage

$ 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]

4 Author

Guanliang MENG

5 Citation

Currently I have no plan to publish msa_cigars.

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.