Metadata-Version: 2.1
Name: extract_specific_sites_from_msa
Version: 0.0.2
Summary: To extract some sites from a multiple sequence alignment. By Guanliang MENG, go to https://github.com/linzhi2013 for more details.
Home-page: https://github.com/linzhi2013
Author: Guanliang Meng
Author-email: mengguanliang@foxmail.com
License: UNKNOWN
Description: # extract_specific_sites_from_msa
        
        ## 1 Introduction
        
        `extract_specific_sites_from_msa` is a tool to extract some sites (or codon) from a multiple sequence alignment.
        
        ## 2 Installation
        
            pip install extract_specific_sites_from_msa
        
        There will be a command `extract_specific_sites_from_msa` created under the same directory as your `pip` command.
        
        ## 3 Usage
        
            usage: extract_specific_sites_from_msa [-h] [-infile <file>]
                                                   [-format {fasta,emboss,stockholm,phylip,phylip-relaxed,clustal}]
                                                   [-outformat {fasta,emboss,stockholm,phylip,phylip-relaxed,clustal}]
                                                   [-outfile <file>] [-config <file>]
                                                   [-codon <int>]
        
            To extract some sites (or codon) from a multiple sequence alignment. By
            Guanliang MENG, go to
            https://github.com/linzhi2013/extract_specific_sites_from_msa for more
            details.
        
            optional arguments:
              -h, --help            show this help message and exit
              -infile <file>        input multiple sequence alignment file
              -format {fasta,emboss,stockholm,phylip,phylip-relaxed,clustal}
                                    input file format [phylip-relaxed]
              -outformat {fasta,emboss,stockholm,phylip,phylip-relaxed,clustal}
                                    output file format [fasta]
              -outfile <file>       outfile
              -config <file>        a file containing the sites to be extracted (1 left-
                                    based). do not support 2-5, you should write 2 3 4 5
                                    instead, the site numbers in config can be on one line
                                    or multiple lines.
              -codon <int>          codon site to be extracted [2]
                
        ## Author
        Guanliang MENG
        
        ## Citation
        Currently I have no plan to publish `extract_specific_sites_from_msa`.
        
        However, since `extract_specific_sites_from_msa` makes use of Biopython, you should cite it if you use msaconverter 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
