Metadata-Version: 2.1
Name: bold-identification
Version: 0.0.15
Summary: To get taxa information of sequences from BOLD system
Home-page: https://github.com/linzhi2013/bold_identification
Author: Guanliang Meng
Author-email: mengguanliang@genomics.cn
License: UNKNOWN
Description: # bold_identification
        
        ## 1 Introduction
        
        see `https://github.com/linzhi2013/bold_identification`.
        
        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 <str> -o <str>
                                                     [-d {COX1,COX1_SPECIES,COX1_SPECIES_PUBLIC,COX1_L640bp,ITS,Plant}]
                                                     [-n <int>] [-b {Firefox,Chrome}]
                                                     [-t <int>] [-r <int>]
        
            To identify taxa of given sequences. Some sequences can fail to get taxon
            information, which can be caused by TimeoutException if your network to the
            BOLD server is bad. Those sequences will be output in the file
            '*.TimeoutException.fasta'. You can: 1) run another searching for those
            sequences directly; 2) change the browser (-b option); 3) lengthen the time to
            wait for each query (-t option); 4) increase submission times (-r option) for
            a sequence. By mengguanliang@genomics.cn. See
            https://github.com/linzhi2013/bold_identification.
        
            optional arguments:
              -h, --help            show this help message and exit
              -i <str>              input fasta file
              -o <str>              outfile
              -d {COX1,COX1_SPECIES,COX1_SPECIES_PUBLIC,COX1_L640bp,ITS,Plant}
                                    database to search [COX1]
              -n <int>              how many first top hits will be output. [1]
              -b {Firefox,Chrome}   browser to be used [Chrome]
              -t <int>              the time to wait for a query [30]
              -r <int>              Maximum submission time for a sequence, useful for
                                    handling TimeOutException. [2]
        
        
        ## 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.
        
        
        ## 5 Citation
        When you use `bold_identification` in your study, please cite:
        
            Guanliang MENG, Chengran ZHOU, Shanlin LIU, Shaoying LIU. Mitogenome and nuclear gene datasets of small mammals on Qinghai-Tibetan Plateau.
        
        
        
        
        
        
        
        
        
        
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
