从genbank文件中提取任何cds、rnra或trna基因序列。
gbseqextractor的Python项目详细描述
GBSeq提取器
1简介
gbseqextractor是从genbank文件中提取任何cds、rnra或trna基因序列的工具。使用Biopython（http://www.biopython.org/）
2安装
pip install gbseqextractor
将在与您的pip命令相同的目录下创建命令gbseqextractor
3用法
$ gbseqextractor
usage: gbseqextractor.py [-h] -f <STR> [-prefix <STR>] [-seqPrefix <STR>]
[-types {CDS,rRNA,tRNA,wholeseq} [{CDS,rRNA,tRNA,wholeseq} ...]]
[-gi] [-p] [-t] [-s] [-l] [-rv] [-F]
extract any CDS or rNRA or tRNA DNA sequences of genes from Genbank file.
Note: the position on ID line is 0 left-most! Seqid will be the value of
'/gene=' or '/product=', if they both were not present, the gene will not be
output!
optional arguments:
-h, --help show this help message and exit
-f <STR> Genbank file
-prefix <STR> prefix of output file.
-seqPrefix <STR> prefix of each seq id. default: None
-types {CDS,rRNA,tRNA,wholeseq} [{CDS,rRNA,tRNA,wholeseq} ...]
what kind of genes you want to extract? wholeseq for
whole fasta seq.[CDS]
-gi use gi number as sequence ID instead of accession
number when gi number is present. (default: accession
number)
-p output the position information on the ID line [False]
-t output the taxonomy lineage on ID line [False]
-s output the species name on the ID line [False]
-l output the seq length on the ID line [False]
-rv reverse and complement the sequences if the gene is on
minus strand [False]
-F only output full length genes [False]
作者
孟冠良
引文
此脚本是软件包的一部分，当您在工作中使用此脚本时，请引用：
MitoZ: A toolkit for mitochondrial genome assembly, annotation and visualization with NGS data. Guangliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu (in manuscript)
同时，由于gbseqextractor利用了Biopython，如果你在工作中使用gbseqextractor，你也应该引用它：
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/。
欢迎加入QQ群-->： 979659372
