version 20201128: 1. Now we can handle compounlocation (feature location with "join")! 2. We can also output the translation for each CDS.
gbseqextractor is a tool to extract any CDS or rNRA or tRNA DNA sequences of genes from Genbank file. with Biopython (http://www.biopython.org/)
pip install gbseqextractor
There will be a command gbseqextractor created under the same directory as your pip command.
$ gbseqextractor
usage: gbseqextractor.py [-h] -f <STR> -prefix <STR> [-seqPrefix <STR>]
[-types {CDS,rRNA,tRNA,wholeseq,gene} [{CDS,rRNA,tRNA,wholeseq,gene} ...]] [-cds_translation]
[-gi] [-p] [-t] [-s] [-l] [-rv] [-F]
Extract any CDS or rNRA or tRNA DNA sequences of genes from Genbank file.
Seqid will be the value of '/gene=' or '/product=', if they both were not
present, the gene will not be output!
version 20201128:
Now we can handle compounlocation (feature location with "join")!
We can also output the translation for each CDS (retrived from '/translation=')
Please cite:
Guanliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu,
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation
and visualization, Nucleic Acids Research, https://doi.org/10.1093/nar/gkz173
optional arguments:
-h, --help show this help message and exit
-f <STR> Genbank file
-prefix <STR> prefix of output file. required.
-seqPrefix <STR> prefix of each seq id. default: None
-types {CDS,rRNA,tRNA,wholeseq,gene} [{CDS,rRNA,tRNA,wholeseq,gene} ...]
what kind of genes you want to extract? wholeseq for whole fasta seq. WARNING: Each sequence in the
result files corresponds to ONE feature in the GenBank file, I will NOT combine multiple CDS of the
same gene into ONE! [CDS]
-cds_translation Also output translated CDS (required -types CDS). The translations are retrived directly from the
'/translation=' key word. [False]
-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. Warning: the position on ID line is 0 left-most!
[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. Always True!
-F only output full length genes,i.e., exclude the genes with '>' or '<' in their location [False]
Guanliang MENG
This script is part of the package MitoZ, when you use the script in your work, please cite:
Guanliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu,
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization, Nucleic Acids Research, https://doi.org/10.1093/nar/gkz173
Meanwhile, since gbseqextractor makes use of Biopython, you should alos cite it if you use gbseqextractor 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.