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        "author": "Brent Pedersen",
        "author_email": "bpederse@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "tools for pedigree files\n------------------------\n\n[![PyPI version](https://badge.fury.io/py/pedagree.svg)](http://badge.fury.io/py/pedagree)\n[![Build Status](https://travis-ci.org/brentp/pedagree.svg?branch=master)](https://travis-ci.org/brentp/pedagree)\n[![Documentation Status](https://readthedocs.org/projects/pedagree/badge/?version=latest)](http://pedagree.readthedocs.org/en/latest/?badge=latest)\n\n\nQuickstart\n----------\n\nMost users will only need to run as a command-line tool with a ped and VCF, e.g:\n\n```\npython -m pedagree --plot --prefix ceph-1463 ceph1463.vcf.gz ceph1463.ped\n```\n\nThat will create 3 QC files and 3 QC plots where `_error` columns will \nindicate:\n+ discrepancies between reported and inferred relations\n+ discrepancies between reported and inferred sex\n+ higher levels of HET calls or more variance in allele frequencies for het calls.\n\nOverview\n--------\n\n\n**NOTE** this module used to be named to \"peddy\".\n\n`pedagree` is a python library for querying, QC'ing, and manipulating pedigree files.\n\nIt currently makes it simple to extract things like:\n\n + parent-child pairs\n + trios\n + sibs\n + stats on number of males/females/trios/affecteds/unaffecteds\n + families.\n + families with at least N members\n + families with at least N children\n + [not yet] families with at least N generations\n + coefficient of relatedness given relation defined in the pedigree.\n\nAlso, given a pedigree file and a VCF file pedagree provides tools to:\n\n + find likely sample mixups (or PED errors)\n   - sex mixups on X-Chrom\n   - family mixups by inferring relatedness with VCF\n\n + find mendelian errors\n\n\nUsage\n-----\n\n```Python\n>>> from pedagree import Ped, SEX, PHENOTYPE\n\n>>> p = Ped('my.ped')\n# not yet.\n#>>> p.dot() # draw the pedigree with graphviz\n\n# not yet\n# find any obvious issues (3 parents, mom as male, etc).\n>>> p.validate()\n\n# number of affecteds, un, males, females, etc. (contingency table?)\n>>> p.summary()\n\n# iterable\n>>> p.samples()\n\n>>> p.samples(phenotype=PHENOTYPE.AFFECTED, sex=SEX.MALE)\n\n# sample object\n>>> s = next(p.samples())\n\n>>> s.phenotype\n\n>>> s.sex\n\n>>> s.mom\n\n>>> s.dad\n\n>>> s.siblings\n\n>>> s.kids\n```\n\nQuality Control\n---------------\n\nIf cyvcf2 is installed, then, given a ped-file and a VCF, we can look for cases where the relationships\ndefined in the ped file do not match the relationships derived from the genotypes in the VCF.\n\n```Python\n>>> from pedagree import Ped\n>>> p = Ped('cohort.ped')\n>>> df = p.ped_check('cohort.vcf.gz')\n>>> df[df.error] # show pairs of samples where the inferred differs from the reported.\n\n```\n\n[![relplot](http://pedagree.readthedocs.org/en/latest/_images/ped-check.png)](http://github.com/brentp/cyvcf2/)\n\nWe don't see any obvious errors in this pedigree. An obvious error would be when a red colored dot clusters with blue dots. \nThe *outlined dots* have a very low IBS0 rate, indicating that they are likely parent-child pairs.\n\nBy looking for the frequency of heterozygotes in the non-PAR regions of\nthe X chromosome, we can determine sex from a VCF:\n\n```Python\n>>> from pedagree import Ped\n>>> p = Ped('cohort.ped')\n>>> p.sex_check('cohort.vcf.gz', plot=True)\n... List of all samples with number of HETs, HOMREF, HOMALT on X\n```\nThis will also create an image like this one where we can\nsee a clear sample mixup.\n\n[![sex_plot](https://raw.githubusercontent.com/brentp/pedagree/master/images/sex_check.png)](http://github.com/brentp/cyvcf2/)\n\n\nOn creating a pedigree object (via Ped('some.ped'). `pedagree` will print warnings to STDERR as appropriate like:\n\n```\npedigree warning: '101811-101811' is dad but has female sex\npedigree warning: '101897-101897' is dad but has female sex\npedigree warning: '101896-101896' is mom of self\npedigree warning: '102110-102110' is mom but has male sex\npedigree warning: '102110-102110' is mom of self\npedigree warning: '101381-101381' is dad but has female sex\npedigree warning: '101393-101393' is mom but has male sex\n\nunknown sample: 102498-102498 in family: K34175\nunknown sample: 11509-11509 in family: K567331\nunknown sample: 5180-5180 in family: K8565\n```",
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