从CDS序列中提取一些密码子位置(1,2,3)。
extract-codon-alignment的Python项目详细描述
提取密码子对齐
1简介
extract-codon-alignment
(https://github.com/linzhi2013/extract_codon_alignment)是一个工具,用于从与Biopython
(http://www.biopython.org/)对齐的cds中提取一些密码子位置(1、2、3)
2安装
$ pip install extract-codon-alignment
# or with Bioconda
conda install extract-codon-alignment
将在与您的pip
命令相同的目录下创建命令extract_codon_alignment
。
3用法
$ 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
作者
孟冠良
引文
目前我没有计划发布extract-codon-alignment
。
但是,由于extract-codon-alignment
使用Biopython
,如果在工作中使用extract-codon-alignment
,则应该引用它:
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
有关详细信息,请转到http://www.biopython.org/
。