Metadata-Version: 1.1
Name: bold-retriever
Version: 0.2.3
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
        ==============
        
        |Pypi index| |Build Status| |Cover alls| |Dependencies status| |Download numbers|
        
        
        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 (python2.7)::
        
            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
        
        .. |Pypi index| image:: https://badge.fury.io/py/bold_retriever.svg
           :target: http://badge.fury.io/py/bold_retriever
        .. |Build Status| image:: https://travis-ci.org/carlosp420/bold_retriever.png?branch=master
           :target: https://travis-ci.org/carlosp420/bold_retriever
        .. |Cover alls| image:: https://img.shields.io/coveralls/carlosp420/bold_retriever.svg
           :target: https://coveralls.io/r/carlosp420/bold_retriever?branch=master
        .. |Dependencies status| image:: https://gemnasium.com/carlosp420/bold_retriever.svg
           :target: https://gemnasium.com/carlosp420/bold_retriever
        .. |Download numbers| image:: https://pypip.in/download/bold_retriever/badge.svg
           :target: https://crate.io/packages/bold_retriever
           :alt: Downloads
        
        
        
        
        History
        -------
        * v0.2.3: Reorganizing columns in output file. Querying the API for family
                  name of taxa.
        * v0.2.2: Killed bug taxon search.
        * v0.2.1: Killed bug in scraping web ``Public_BIN`` for species ID.
        * v0.2.0: Scraping web ``Public_BIN`` for species ID.
        * v0.1.9: Added request_id test and option to run fuction in debug mode.
        * v0.1.8: Fixed bug for exception when BOLD sends empty list of taxon names.
        * v0.1.7: Fixed bug for exception when BOLD sends empty list of taxon names.
        * v0.1.6: Append taxon identification results to file as we get them.
        * v0.1.5: Additionat tests coverage 92%
        * v0.1.4: Fixed bug in taxon_search function
        * 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":[]}``.
        
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
