bold-identification 0.0.18

To get taxa information of sequences from BOLD system

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.

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> [-f <str>] -o <str>
                           [-d {COX1,COX1_SPECIES,COX1_SPECIES_PUBLIC,COX1_L640bp,ITS,Plant}]
                           [-n <int>] [-b {PhantomJS,Firefox,Chrome}]
                           [-t <int>] [-r <int>] [-c] [-D] [-H]

To identify taxa of given sequences from BOLD (http://www.boldsystems.org/).
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 with the same command directly (-c option);
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.

Also, the sequences without BOLD matches will be output in the
file '*.NoBoldMatchError.fasta'

By [e-mail].
See https://github.com/linzhi2013/bold_identification.


optional arguments:
  -h, --help            show this help message and exit
  -i <str>              input file name
  -f <str>              input file format [fasta]
  -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 {PhantomJS,Firefox,Chrome}
                        browser to be used [PhantomJS]
  -t <int>              the time to wait for a query [60]
  -r <int>              Maximum submission time for a sequence, useful for
                        handling TimeOutException. [4]
  -c                    continuous mode, jump over the ones already in "-o"
                        file, will resubmit all the remained. [False]
  -D                    debug mode output [False]
  -H                    No graphical window mode, possibly not work for "-b
                        Firefox", has no effect on "-b PhantomJS". [False]

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.
if this happens with '-H' option, try not to use it.

5 Citation

When you use bold_identification in your study, please cite:

Guanliang MENG, Chengran ZHOU, et al., Shanlin LIU, Shaoying LIU. Mitogenome and nuclear gene datasets of small mammals on Qinghai-Tibetan Plateau.