Metadata-Version: 1.1
Name: pygenomes
Version: 0.1.0
Summary: a command-line tool for downloading genome data from UCSC ftp site.
Home-page: https://github.com/TinyNecessaryTools/Biology
Author: FEI YUAN
Author-email: fyuan4@uh.edu
License: MIT
Download-URL: https://github.com/TinyNecessaryTools/Biology/pygenomes/dist/pygenomes-0.1.0.tar.gz
Description: `pygenomes` (formally named `pygenomes`) is a Python module and also a command-
        line tool for downloading genome data from UCSC ftp site. 
        
        Using this tool you can easily check available taxa or available groups of 
        taxa by simply typing the name of the tool or add ``-g`` flag with a group 
        name. 
        
        Download genome or chromosome data with this tool also very simple. You can 
        download data by using commom name, scientific name, or even specific assembly 
        name (e.g. ``human``, ``Homo sapiens``, ``hg38``). 
        
        If there is available data in the ftp site, you also can downlaod data via 
        interactive mode, which will allow you to choose specific genome assembly.To 
        do this, you only need to assign a True value for assembly, then according to 
        the available list prompted to you simply input the interested assembly.
        
        
        Features
        --------
        
        - Install a Python module named ``pygenomes.py``
        - Install a Python command-line script named ``pygenomes``
        - Easily check available taxa and genomes in commend-line
        - Simply download genomes via comman, scientific, or assembly name
        - Using interactive mode, simply download specific assembly genome
        - Easily download genome and chromosome in specific file format
        - Pure Python module and without any third-party dependence
        
        
        Examples
        --------
        
        You can use `pygenomes` as a Python module e.g. like in the following
        interactive Python session (the function's signature might still change 
        a bit in the future)::
        
            >>> from pygenomes import genomes
            >>>
            # prints out available taxa in group of mammals
            >>> genomes(gname=[group_name])                    # i.e. ['mammals']
            # download human reference genome (hg19) in .2bit format
            >>> genomes(taxa=[taxa])                           # i.e. ['human']
            # interactive mode, ask for inputing and downloading specific assembly
            >>> genomes(taxa=[taxa], assembly=[assembly])      # i.e. ['cow'], ['1']
            # try to download chromosome data, per fa.gz file per chromosome
            >>> genomes(taxa=[taxa], chrs=[format])            # i.e. ['cow'], ['1']
        
        In addition there is a script named ``pygenomes``, which can be used 
        more easily from the system command-line like this (you can see many 
        more examples when typing ``pygenomes -h`` on the command-line)::
        
            $ pygenomes -g -1                 # prints out all available taxa
        
            $ pygenomes -g mammal             # prints out all available taxa in group 
                                                of mammal
            $ pygenomes -t yeast              # download yeast reference genome in 
                                                .2bit format
            $ pygenomes -t yeast -a 1         # interactive mode, ask for inputing and 
                                                downloading specific assembly
            $ pygenomes -t cow -f fa.gz       # try to download cow reference genome 
                                                in fa.gz format
            $ pygenomes -t dog -a 1 -o /tmp   # interactive mode, ask for inputing, 
                                                file will be stored in /tmp
            $ pygenomes -t cat -c 1           # download cat chromosome data, per 
                                                chromosome per fa.gz file
        
Keywords: genome,download,ucsc,bioinformatic,biology
Platform: Posix
Platform: Windows
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: End Users/Desktop
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX
Classifier: Operating System :: Microsoft :: Windows
Classifier: Programming Language :: Python
Classifier: Topic :: Utilities
