Skip to main content

To return CIGAR strings of a multiple sequences alignment

Project description

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.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

msa_cigars-0.0.1.tar.gz (18.3 kB view hashes)

Uploaded source

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page