Metadata-Version: 1.1
Name: eutils
Version: 0.0.3
Summary: Structured Python interface to NCBI E-Utilities.
Home-page: https://bitbucket.org/invitae/eutils
Author: Reece Hart
Author-email: reecehart+eutils@gmail.com
License: Apache
Description: ====================================================
        eutils -- a simplified interface to NCBI E-Utilities
        ====================================================
        
        eutils is a Python package dedicated to searching for, fetching, and
        parsing records from NCBI using their E-utilities_ interface.
        
        STATUS: This code is alpha. There are no known bugs, but the code supports
        only a limited subset of E-Utilities replies
        
        
        Features
        --------
        * optional sqlite-based caching of compressed replies
        * automatic throttling
        * simple Pythonic interface for searching and fetching
        * "façades" over XML from replies provide access to essential attributes
        
        A Quick Example
        ---------------
        
        ::
        
          In [1]: import eutils.client
          
          In [2]: esr = ec.esearch(db='gene',term='tumor necrosis factor')
          
          In [3]: gb = ec.efetch(db='gene',id=esr.ids[0])
          
          In [4]: gb.locus, gb.maploc, gb.description, gb.type
          Out[4]: ('TP53', '17p13.1', 'tumor protein p53', 'protein-coding')
        
          In [5]: [ str(r) for r in gb.references ]
          Out[5]: 
          ['GeneCommentary(acv=NC_000017.10,type=genomic,heading=Reference GRCh37.p13 Primary Assembly,label=chromosome 17 reference GRCh37.p13 Primary Assembly)',
           'GeneCommentary(acv=NG_017013.2,type=genomic,heading=Reference assembly,label=RefSeqGene)',
           'GeneCommentary(acv=NC_018928.2,type=genomic,heading=Alternate CHM1_1.1,label=chromosome 17 alternate CHM1_1.1)',
           'GeneCommentary(acv=AC_000149.1,type=genomic,heading=Alternate HuRef,label=chromosome 17 alternate HuRef)']
          
          In [6]: gb.references[0].acv
          Out[6]: 'NC_000017.10'
          
          In [7]: gb.references[0].products[0].acv
          Out[7]: 'NM_001126112.2'
          
          In [8]: gb.references[0].products[0].genomic_coords.strand
          Out[8]: -1
        
          In [9]: gb.references[0].products[0].genomic_coords.intervals
          Out[9]: 
          [(7590694, 7590868),
           (7579838, 7579937),
           (7579699, 7579721),
           (7579311, 7579590),
           (7578370, 7578554),
           (7578176, 7578289),
           (7577498, 7577608),
           (7577018, 7577155),
           (7576852, 7576926),
           (7573926, 7574033),
           (7571719, 7573008)]
          
          
        
        .. _E-utilities: http://www.ncbi.nlm.nih.gov/books/NBK25499/
        
Keywords: bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Healthcare Industry
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python
Classifier: Topic :: Database :: Front-Ends
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
