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To get taxa information of sequences from BOLD system

Project description

bold_identification

Important

This package relies on Python3. 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.

Currently, bold_identification only runs on Mac OS, Windows 64bit, Linux.

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,MATK_RBCL}]
                          [-n <int>] [-r <int>] [-c] [-D] [--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) lengthen the time to wait for each query (-t option);
3) increase submission times (-r option) for a sequence.

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

By mengguanliang AT genomics DOT cn.
See https://github.com/linzhi2013/bold_identification.

version: 0.0.22

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,MATK_RBCL}
                        database to search [COX1]
  -n <int>              how many first top hits will be output. [1]
  -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]
  --version             show program's version number and exit

4 Citation

When you use bold_identification in your study, please cite:

Yang, Chentao, Shangjin Tan, Guanliang Meng, David G. Bourne, Paul A. O'brien, Junqiang Xu, Sha Liao, Ao Chen, Xiaowei Chen, and Shanlin Liu. "Access COI barcode efficiently using high throughput Single End 400 bp sequencing." BioRxiv (2018): 498618. DOI: 10.1101/498618

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