Metadata-Version: 1.1
Name: peddy
Version: 0.0.2
Summary: pleasingly pythonic pedigree manipulation
Home-page: UNKNOWN
Author: Brent Pedersen
Author-email: bpederse@gmail.com
License: UNKNOWN
Description: tools for pedigree files
        ------------------------
        
        [![PyPI version](https://badge.fury.io/py/peddy.svg)](http://badge.fury.io/py/peddy)
        [![Build Status](https://travis-ci.org/brentp/peddy.svg?branch=master)](https://travis-ci.org/brentp/peddy)
        
        This is currently under development. It already has a nice API for dealing with pedigree files.
        
        It currently makes it simple to extract things like:
        
         + parent-child pairs
         + trios
         + sibs
         + stats on number of males/females/trios/affecteds/unaffecteds
         + families.
         + families with at least N members
         + families with at least N children
         + [not yet] families with at least N generations
        
        
        We are working on adding support for the following:
        
        Given a pedigree file and a VCF file:
        
         + find likely sample mixups (or PED errors)
           - gender mixups on X-Chrom
           - family mixups by inferring relatedness with VCF
        
         + mendelian errors
        
        
        Usage
        -----
        
        ```Python
        >>> from peddy import Ped, SEX, PHENOTYPE
        
        >>> p = Ped('my.ped')
        # not yet.
        #>>> p.dot() # draw the pedigree with graphviz
        
        # not yet
        # find any obvious issues (3 parents, mom as male, etc).
        >>> p.validate()
        
        # number of affecteds, un, males, females, etc. (contingency table?)
        >>> p.summary()
        
        # iterable
        >>> p.samples()
        
        >>> p.samples(phenotype=PHENOTYPE.AFFECTED, sex=SEX.MALE)
        
        # sample object
        >>> s = next(p.samples())
        
        >>> s.phenotype
        
        >>> s.sex
        
        >>> s.mom
        
        >>> s.dad
        
        >>> s.siblings
        
        >>> s.kids
        ```
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
