peddy 0.0.2

pleasingly pythonic pedigree manipulation

tools for pedigree files
------------------------

[](http://badge.fury.io/py/peddy)
[](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
```