返回多序列对齐的雪茄字符串
msa-cigars的Python项目详细描述
MSA_雪茄
1简介
msa_cigars是获取多序列比对雪茄的工具。假设输入文件中有一个对齐！雪茄是按照参照顺序。孟冠良，见https://github.com/linzhi2013/msa_cigars。
2安装
pip install msa_cigars
将在与您的pip命令相同的目录下创建命令msa_cigars。
3用法
$ 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作者
孟冠良
5条引文
目前我没有计划发布msa_cigars。
但是，由于msa_cigars使用Biopython，如果在工作中使用breakSeqInNs_then_translate，也应该引用它：
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/。
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