Metadata-Version: 2.1
Name: gbseqextractor
Version: 0.0.3
Summary: Extract any CDS or rNRA or tRNA DNA sequences of genes from Genbank file.
Home-page: https://github.com/linzhi2013
Author: Guanliang Meng
Author-email: linzhi2012@gmail.com
License: UNKNOWN
Description: # gbseqextractor
        
        # updates
        version 20201128:
                Now we can handle compounlocation (feature location with "join")!
        
        
        ## 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} ...]] [-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")!
        
            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!
        
            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.[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. 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.
        
        
        
        
        
        
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Requires-Python: >=3
Description-Content-Type: text/markdown
