Metadata-Version: 1.1
Name: bold_retriever
Version: 0.1.2
Summary: It queries the BOLD database to get identification of taxa based on COI sequences
Home-page: https://github.com/carlosp420/bold_retriever
Author: Carlos Pena
Author-email: mycalesis@gmail.com
License: GPL v3
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
        -------
        
        * v0.1.2: 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":[]}``.
Keywords: bold_retriever
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Environment :: Console
Classifier: Programming Language :: Python :: 2.7
