Metadata-Version: 2.1
Name: pydbsnp
Version: 0.1.9
Summary: Interface with dbSNP VCF data
Home-page: https://github.com/anthony-aylward/pydbsnp.git
Author: Anthony Aylward
Author-email: aaylward@eng.ucsd.edu
License: UNKNOWN
Description: # pydbsnp
        
        Interface with dbSNP VCF data
        
        ## Installation
        
        First install the python package via `pip3`
        
        ```sh
        pip3 install pydbsnp
        ```
        or
        ```sh
        pip3 install --user pydbsnp
        ```
        
        Once the python package is installed, download and index the dbSBP VCF data:
        
        ```sh
        pydbsnp-download
        pydbsnp-index
        ```
        
        For hg19/GRCh37 coordinates:
        
        ```sh
        pydbsnp-download --reference-build GRCh37
        pydbsnp-index
        ```
        
        ## Command line usage
        
        ```sh
        pydbsnp-query -h
        ```
        
        ```sh
        pydbsnp-query rs231361
        pydbsnp-query chr8:118184783
        pydbsnp-query --reference-build GRCh37 rs231361
        pydbsnp-query rs231361 chr8:118184783 rs7903146
        ```
        
        ## API
        
        Two classes are provided: `Variant` and `GeneralizedVariant`.
        
        An object of the `Variant` class has an attribute for each relevant field
        of the VCF.
        ```python
        from pydbsnp import Variant
        v = Variant(id='rs8056814')
        print(v.chrom, v.pos, v.id, v.ref, v.alt)
        print(v.info)
        w = Variant(id='rs8056814', reference_build='GRCh37')
        print(w.chrom, w.pos)
        x = Variant('chr16', 75218429)
        print(x)
        help(Variant)
        ```
        
        An object of the `GeneralizedVariant` class is similar, but each attribute
        is a tuple which may have multiple items. For example, one RSID may map
        to two sets of coordinates.
        ```python
        gv = GeneralizedVariant(id='rs8056814')
        print(gv.chrom, gv.pos, gv.id, gv.ref, gv.alt)
        ```
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
