Metadata-Version: 2.1
Name: msa_cigars
Version: 0.0.1
Summary: To return CIGAR strings of a multiple sequences alignment
Home-page: https://github.com/linzhi2013/
Author: Guanliang Meng
Author-email: mengguanliang@foxmail.com
License: UNKNOWN
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.
        
        
        
        
        
        
        
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Requires-Python: >=3
Description-Content-Type: text/markdown
