https://github.com/linzhi2013/msa_cigars

A tool to get the CIGARs of a multiple sequence alignment.
https://github.com/linzhi2013/msa_cigars

alignment biopython cigars msa

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A tool to get the CIGARs of a multiple sequence alignment.

• Host: GitHub
• URL: https://github.com/linzhi2013/msa_cigars
• Owner: linzhi2013
• License: gpl-3.0
• Created: 2018-08-13T09:04:39.000Z (almost 8 years ago)
• Default Branch: master
• Last Pushed: 2021-09-23T13:03:52.000Z (over 4 years ago)
• Last Synced: 2025-12-26T14:01:00.780Z (5 months ago)
• Topics: alignment, biopython, cigars, msa
• Size: 34.2 KB
• Stars: 2
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# 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  -refseq_id  [-n ] [-g ]

                     [-f ] [-o ]

        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          input msa file

          -refseq_id   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           character of unknown base [N]

          -g           character of gap base [-]

          -f        the msa format [fasta]

          -o          outfile name [stdout]

## 4 Author

Guanliang MENG

## 5 Citation

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.