Metadata-Version: 2.1
Name: bold-identification
Version: 0.0.7
Summary: To get taxa information of sequences from BOLD system
Home-page: http://mengguanliang.com
Author: Guanliang Meng
Author-email: mengguanliang@genomics.cn
License: UNKNOWN
Description: # bold_identification
        
        ## 1 Introduction
        This is a package which can get the taxonomy information of sequences from BOLD [http://www.boldsystems.org/index.php](http://www.boldsystems.org/index.php).
        
        To get the taxonomy information of a sequence from BOLD, what we usually do is: (1) open the website `http://www.boldsystems.org/index.php/IDS_OpenIdEngine` with a browser; (2) Choose a database; (3) input the sequence (4) click `submit` and wait for the result. (5) Copy the taxonomy information from the result page.
        
        `bold_identification` actually does the same things as above, but it does such a thing automatically for you, and makes life easier.
        
        
        Currently, `bold_identification` only runs on Mac OS, Windows 64bit, Linux.
        
        But be ware, only the Chrome browser works on Windows, while FireFox doesn't.
        
        ## 2 Installation
        
            pip3 install bold_identification
        
        There will be a command `bold_identification` created under the same directory as your `pip3` command.
        
        ## 3 Usage
        run `bold_identification`
        
        
            usage: bold_identification [-h] -i INFILE -o OUTFILE
                                       [-d {COX1,COX1_SPECIES,COX1_SPECIES_PUBLIC,COX1_L640bp,ITS,Plant}]
                                       [-b {Firefox,Chrome}] [-t TIMEOUT]
        
            To identify taxa of given sequences. If some sequences fail to get taxon
            information, you can run another searching for those sequences. This can be
            caused by TimeoutException if your network to the BOLD server is bad. Or you
            can lengthen the time to wait for each query (-t option). By
            mengguanliang@genomics.cn.
        
            optional arguments:
              -h, --help            show this help message and exit
              -i INFILE             input fasta file
              -o OUTFILE            outfile
              -d {COX1,COX1_SPECIES,COX1_SPECIES_PUBLIC,COX1_L640bp,ITS,Plant}
                                    database to search [COX1]
              -b {Firefox,Chrome}   browser to be used [Firefox]
              -t TIMEOUT            the time to wait for a query [30]
        
        
        ## 4 Problems
        
        ### Cannot download the browsers
        This can happen when your network is not good.   
        
        Solution:   
        Download the executable driver file manaully, then extract the executable and put it on the `drivers` directory. See more details output by `bold_identification` when you run into this problem.
        
        ### Browser doen't work
        Sometimes it happens to me. And I don't know why. I guess it is because the browser driver is not so stable.
        
        Solution:   
        Try another browser with the `-b` option.
        
        
        
        
        
        
        
        
        
        
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: >=3.4
Description-Content-Type: text/markdown
