gbseqextractor

updates

version 0.0.5:
Merge pull request #4 from gopalpeddinti/patch-1. This was needed to fix the BioPython deprecation warning.

version 20201128:
1. Now we can handle compounlocation (feature location with "join")!
2. We can also output the translation for each CDS.

1 Introduction

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/)

2 Installation

pip install gbseqextractor

There will be a command gbseqextractor created under the same directory as your pip command.

3 Usage

$ 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]

Author

Guanliang MENG

Citation

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.