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/)
$ 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.
$ 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
Guanliang MENG
Currently I have no plan to publish extract-codon-alignment
. 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!!!
Besides, 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.