This notebook is to test the inheritance machinery in gemini. Families are drawn in an image where

Affection

white fill means unaffected
gray fill means unknown
black fill means affected

genotype status is labelled in the image.

See this issue for discussion along with this gist



In [1]:

    
import gemini.tests
from gemini.tests.test_inheritance import TestFamily, family
Sample = family.Sample
HOM_REF, HET, UNKNOWN, HOM_ALT = range(4)



In [2]:

    
fam = TestFamily("""
 #family_id  sample_id   paternal_id maternal_id sex phenotype
 1   dad   0   0   1  1
 1   mom   grandpa   grandma   2  1
 1   kid   dad   mom   1  2
 1   kid2   dad   mom   1  1
 1   grandma 0   0     2  1
 1   grandpa 0   0     1  1""")
fam.gt_types = [HET, HET, HOM_ALT, HET, HET, HET]
fam.gt_depths = [20, 20, 20, 20, 20, 20]
fam.draw(tests=("auto_rec", ))









    



auto_rec
--------
default             	True
strict=False        	True
only_affected=False 	True
both False          	True

Autosomal Recessive



In [3]:

    
# if we set anyone else to HOM_ALT, it's no longer auto_rec unless only-affected is False:

# set grandpa to HOM_ALT
fam.gt_types[5] = HOM_ALT
fam.draw(tests=("auto_rec"))









    



auto_rec
--------
default             	False
strict=False        	False
only_affected=False 	True
both False          	True



In [4]:

    
# set grandpa back to het
fam.gt_types[5] = HET
# can require a greater read depth (note we set all samples to have depth 20 above)
fam.auto_rec(min_depth=12), fam.auto_rec(min_depth=22)









    Out[4]:





(True, False)



In [5]:

    
# if we set someone else to affected... the sibling. it can never be auto_rec:
fam.subjects[3].affected = True
fam.draw(tests=("auto_rec",))









    



auto_rec
--------
default             	False
strict=False        	False
only_affected=False 	False
both False          	False

Autosomal Dominant



In [6]:

    
fam.gt_types = [HET, HET, HOM_ALT, HET, HOM_REF, HOM_REF]
fam.draw(tests=("auto_dom"))
# parents arent affected...









    



auto_dom
--------
default             	False
strict=False        	False
only_affected=False 	False
both False          	False



In [7]:

    
fam.de_novo(strict=False) # even though mom is a de-novo?









    Out[7]:





False



In [8]:

    
for s in fam.subjects: s.affected = True
fam.draw(tests=("auto_dom"))









    



auto_dom
--------
default             	False
strict=False        	False
only_affected=False 	False
both False          	False



In [9]:

    
fam.subjects[5].affected = fam.subjects[4].affected = False
fam.draw()
# still not auto_dom because affected is homalt









    



auto_rec
--------
default             	False
strict=False        	False
only_affected=False 	False
both False          	False

auto_dom
--------
default             	False
strict=False        	False
only_affected=False 	False
both False          	False






    



WARNING: auto-recessive called on family 1 where no affected has parents
WARNING: auto-recessive called on family 1 where affected has affected parents
WARNING: auto-recessive called on family 1 where no affected has parents
WARNING: auto-recessive called on family 1 where affected has affected parents



In [10]:

    
fam.gt_types[2] = HET
fam.draw(tests=("auto_dom",))









    



auto_dom
--------
default             	False
strict=False        	False
only_affected=False 	False
both False          	False



In [11]:

    
# TODO: check this
ffd = family.Family([Sample("mom", True, "female"), Sample("dad", False, "male"),
                    Sample("kid", True, "male")], "fam")
ffd.subjects[2].mom = ffd.subjects[0]
ffd.subjects[2].dad = ffd.subjects[1]

ffd = TestFamily(ffd)
ffd.gt_types = [HET, HOM_ALT, HET]
# dad is homalt, so only works under only_affected=False
ffd.draw(tests=("auto_dom",))

ffd.gt_types = [HET, HOM_REF, HET]
ffd.draw(tests=("auto_dom",))









    



auto_dom
--------
default             	False
strict=False        	False
only_affected=False 	True
both False          	True






    












    



auto_dom
--------
default             	True
strict=False        	True
only_affected=False 	True
both False          	True

with unknowns



In [12]:

    
fam3 = TestFamily("""
 #family_id  sample_id   paternal_id maternal_id sex phenotype
 1   dad   0   0   1  2
 1   mom   grandpa   grandma   2  -9
 1   kid   dad   mom   1  2
""")
fam3.gt_types = [HET, HET, HET]
fam3.gt_depths = [20, 20, 20]
fam3.draw(tests=("auto_dom",))









    



auto_dom
--------
default             	False
strict=False        	True
only_affected=False 	False
both False          	True

De Novo



In [13]:

    
# not a de_novo because parents have it.
fam3.draw(tests=("de_novo",))









    



de_novo
-------
default             	False
strict=False        	False
only_affected=False 	False
both False          	False



In [14]:

    
# should never be de_novo, because mom has it
fam3.gt_types = [HOM_REF, HOM_ALT, HET]
fam3.subjects[0].affected = False
fam3.subjects[1].affected = False
fam3.subjects[2].affected = True
fam3.draw(tests=("de_novo",))









    



de_novo
-------
default             	False
strict=False        	False
only_affected=False 	False
both False          	False



In [15]:

    
# should never be auto_dom (at least not this generation. since it's de_novo).
fam3.gt_types = [HOM_REF, HOM_REF, HET]

fam3.draw(tests=("auto_dom",))









    



auto_dom
--------
default             	False
strict=False        	False
only_affected=False 	False
both False          	False



In [16]:

    
ff = family.Family([Sample("mom", False, "female"), Sample("dad", False, "male"),
            Sample("kid", True, "male")], "fam")
ff.subjects[2].mom = ff.subjects[0]
ff.subjects[2].dad = ff.subjects[1]

ff = TestFamily(ff)
ff.gt_types = [HOM_ALT, HOM_ALT, HET]
ff.draw(tests=("de_novo",))









    



de_novo
-------
default             	True
strict=False        	True
only_affected=False 	True
both False          	True



In [17]:

    
# unaffected sibling is a HET.

ff = family.Family([Sample("mom", False, "female"), Sample("dad", False, "male"),
            Sample("kid", True, "male"), Sample("kid2", False, "male")], "fam")
ff.subjects[2].mom = ff.subjects[0]
ff.subjects[2].dad = ff.subjects[1]
ff.subjects[3].mom = ff.subjects[0]
ff.subjects[3].dad = ff.subjects[1]

ff = TestFamily(ff)
ff.gt_types = [HOM_ALT, HOM_ALT, HET, HET]
ff.draw(tests=("de_novo",))









    



de_novo
-------
default             	False
strict=False        	False
only_affected=False 	True
both False          	True



In [ ]: