bold-identification 0.0.9

To get taxa information of sequences from BOLD system

bold_identification

1 Introduction

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 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
[e-mail].

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.