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To get taxa information of sequences from BOLD system

Project description

bold_identification

Important

This package relies on Python3.5 or hihger version. If you do not have Python3 installed, please intall it first. If you do not know how to install Python packages, please refer to https://packaging.python.org/tutorials/installing-packages/. Please go to https://docs.python.org/3/ to learn more about Python. I cannot offer any support for such kind of problems.

1 Introduction

see https://github.com/linzhi2013/bold_identification.

This is a Python3 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.

Beware,

  • only the Chrome browser and PhantomJS browser work on Windows, while FireFox doesn't.

  • Only PhantomJS browser can be run on a non-graphical computer, while Chrome and FireFox cannot, even though there is a '-H' option.

2 Installation

pip install bold_identification

There will be a command bold_identification created under the same directory as your pip 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>] [-t2 <int>] [-r <int>] [-c] [-D] [-H]
                           [--version]

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 (but add -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 mengguanliang@genomics.cn.
See https://github.com/linzhi2013/bold_identification.

Notes:

It seems that PhantomJS sometimes doesn't work when search Plant and Fungi
databases. If this happens, you can try another browser.

version: 0.0.20

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]
  -t2 <int>             the extra time to wait for ITS or Plant query [10]
  -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. use "-cc" to
                        also jump over the ones in "*.NoBoldMatchError.fasta"
                        file. [False]
  -D                    debug mode output [False]
  -H                    No graphical window mode, possibly not work for "-b
                        Firefox", has no effect on "-b PhantomJS". [False]
  --version             show program's version number and exit

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.

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