Metadata-Version: 2.1
Name: extract-codon-alignment
Version: 0.0.1
Summary: To extract some codon positions (1st, 2nd, 3rd) from a CDS alignment.
Home-page: https://github.com/linzhi2013/extract_codon_alignment
Author: Guanliang Meng
Author-email: linzhi2012@gmail.com
License: UNKNOWN
Description: # extract-codon-alignment
        
        ## 1 Introduction
        
        `extract-codon-alignment`  (https://github.com/linzhi2013/extract_codon_alignment) is a tool to extract some codon positions (1st, 2nd, 3rd) from a CDS alignment with `Biopython` (http://www.biopython.org/)
        
        ## 2 Installation
        
            $ pip install extract-codon-alignment
            # or with Bioconda
            conda install extract-codon-alignment
        
        There will be a command `extract_codon_alignment` created under the same directory as your `pip` command.
        
        ## 3 Usage
        
            $ extract_codon_alignment
            usage: extract_codon_alignment [-h] --alignedCDS <file>
                                           [--aln_format <format>]
                                           [--codonPoses {1,2,3,12,13,23}] --outAln <file>
        
            To extract some codon positions (1st, 2nd, 3rd) from a CDS alignment.
        
            optional arguments:
              -h, --help            show this help message and exit
              --alignedCDS <file>   The CDS alignment.
              --aln_format <format>
                                    the file format for the CDS alignment. Anything
                                    accepted by BioPython is fine [fasta]
              --codonPoses {1,2,3,12,13,23}
                                    Codon position(s) to be extracted [12]
              --outAln <file>       output file name
        
        ## Author
        Guanliang MENG
        
        ## Citation
        Currently I have no plan to publish `extract-codon-alignment`.
        
        However, since `extract-codon-alignment` makes use of `Biopython`, you should cite it if you use `extract-codon-alignment` 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
