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To get taxa information of sequences from BOLD system

Project 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.

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

Currently I have no plan to publish bold_identification.

Project details


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bold_identification-0.0.12.tar.gz (20.1 kB) Copy SHA256 hash SHA256 Source None Sep 6, 2018

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