Documentation for pandas-genomics

Version

0.11.0

Pandas ExtensionArray for working with genomics data

Quickstart

Variant objects holds information about a particular variant:

>>> from pandas_genomics.scalars import Variant
>>> variant = Variant('12', 112161652, id='rs12462', ref='A', alt=['C', 'T'], score=30)
>>> print(variant)
rs12462(n2)[chr=12;pos=112161652;ref=A;alt=C,T]Q30

Genotype objects are associated with a particular Variant:

>>> gt = variant.make_genotype("A", "C")
>>> print(gt)
A/C

The GenotypeArray stores genotypes with an associated variant and has useful methods and properties. The genotype Series accessor allows those methods and properties to be accessed from a Series.

>>> from pandas_genomics.scalars import Variant
>>> from pandas_genomics.arrays import GenotypeArray
>>> variant = Variant('12', 112161652, id='rs12462', ref='A', alt=['C'])
>>> gt_array = GenotypeArray([variant.make_genotype_from_str(s) for s in ["C/C", "A/C", "A/A"]])

>>> print(gt_array)
<GenotypeArray>
[Genotype(variant=rs12462[chr=12;pos=112161652;ref=A;alt=C])[C/C],
 Genotype(variant=rs12462[chr=12;pos=112161652;ref=A;alt=C])[A/C],
 Genotype(variant=rs12462[chr=12;pos=112161652;ref=A;alt=C])[A/A]]
Length: 3, dtype: genotype(2n)[12; 112161652; rs12462; A; C]

>>> print(gt_array.astype(str))
['C/C' 'A/C' 'A/A']

>>> print(gt_array.encode_dominant())
<IntegerArray>
[1.0, 1.0, 0.0]
Length: 3, dtype: float

>>> print(pd.Series(gt_array).genotype.encode_dominant())
0    1.0
1    1.0
2    0.0
Name: rs12462_C, dtype: float

>>> print(pd.Series(gt_array).genotype.variant)
rs12462[chr=12;pos=112161652;ref=A;alt=C]

>>> print(pd.Series(gt_array).genotype.gt_scores)
[nan nan nan]

>>> import pandas as pd
>>> print(pd.Series(gt_array).genotype.encode_codominant())
0    Hom
1    Het
2    Ref
Name: rs12462_C, dtype: category
Categories (3, object): ['Ref' < 'Het' < 'Hom']

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