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It queries the BOLD database to get identification of taxa based on COI sequences

Project description

==============
Bold Retriever
==============

.. image:: https://badge.fury.io/py/bold_retriever.svg
:target: http://badge.fury.io/py/bold_retriever

.. image:: https://travis-ci.org/carlosp420/bold_retriever.png?branch=master
:target: https://travis-ci.org/carlosp420/bold_retriever

.. image:: https://img.shields.io/coveralls/carlosp420/bold_retriever.svg
:target: https://coveralls.io/r/carlosp420/bold_retriever?branch=master


This script accepts FASTA files containing COI sequences. It queries the BOLD
database http://boldsystems.org/ in order to get the taxa identification
based on the sequences.

Run this way
------------
* clone repository::

cd $USERAPPL
git clone https://github.com/carlosp420/bold_retriever.git

* install dependencies::

cd bold_retriever
module load biopython-env
pip install -r requirements.txt

* run software

You have to choose one of the databases available from BOLD
http://www.boldsystems.org/index.php/resources/api?type=idengine
and enter it as argument:

* COX1_SPECIES
* COX1
* COX1_SPECIES_PUBLIC
* COX1_L640bp

For example::

python bold_retriever.py -f ZA2013-0565.fasta -db COX1_SPECIES

* output::

bold_id seq_id similarity collection_country division taxon class order family
FIDIP558-11 TE-14-27_FHYP_av 0.9884 Finland animal Diptera Insecta Diptera None
GBDP6413-09 TE-14-27_FHYP_av 0.9242 None animal Ornithomya anchineura Insecta Diptera Hippoboscidae
GBDP2916-07 TE-14-27_FHYP_av 0.922 None animal Stenepteryx hirundinis Insecta Diptera Hippoboscidae
GBDP2919-07 TE-14-27_FHYP_av 0.9149 None animal Ornithomya biloba Insecta Diptera Hippoboscidae
GBDP2908-07 TE-14-27_FHYP_av 0.9078 None animal Ornithoctona sp. P-20 Insecta Diptera Hippoboscidae
GBDP2918-07 TE-14-27_FHYP_av 0.9076 None animal Ornithomya chloropus Insecta Diptera Hippoboscidae
GBDP2935-07 TE-14-27_FHYP_av 0.8936 None animal Crataerina pallida Insecta Diptera Hippoboscidae
GBMIN26225-13 TE-14-27_FHYP_av 0.8889 None animal Lucilia sericata Insecta Diptera Calliphoridae
GBDP5820-09 TE-14-27_FHYP_av 0.8833 None animal Coenosia tigrina Insecta Diptera Muscidae
GBMIN26204-13 TE-14-27_FHYP_av 0.883 None animal Lucilia cuprina Insecta Diptera Calliphoridae
GBMIN18768-13 TE-14-27_FHYP_av 0.8823 Brazil animal Ornithoctona erythrocephala Insecta Diptera Hippoboscidae

Full documentation
------------------
See the full documentation at http://bold-retriever.readthedocs.org

See additional usage info in :ref:`usage-label`.

.. include:: ../HISTORY.rst




History
-------

* v0.1.3: Coverage 75%
* v0.1.2: Pep8 and test coverage 69%
* v0.1.1: Packaged as Python module.
* v0.1.0: You can specify which BOLD datase should be used for BLAST of FASTA sequences.
* v0.0.7: Catching exception for NULL, list and text returned instead of XML from BOLD.
* v0.0.6: Catching exception for malformed XML from BOLD.
* v0.0.5: Catch exception when BOLD sends funny data such as ``{"481541":[]}``.

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