BiocFrame 0.3.15

Flexible dataframe representation to support nested structures.

BiocFrame

This package provides BiocFrame class, an alternative to Pandas DataFrame's.

BiocFrame makes no assumption on the types of the columns, the minimum requirement is each column implements length: __len__ and slice: __getitem__ dunder methods. This allows BiocFrame to accept nested representations or any supported class as columns.

To get started, install the package from PyPI

pip install biocframe

Usage

To construct a BiocFrame object, simply provide the data as a dictionary.

from random import random
from biocframe import BiocFrame

obj = {
    "ensembl": ["ENS00001", "ENS00002", "ENS00003"],
    "symbol": ["MAP1A", "BIN1", "ESR1"],
}
bframe = BiocFrame(obj)
print(bframe)

## output
BiocFrame with 3 rows & 2 columns
┏━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┓
┃ ensembl <list> ┃ symbol <list> ┃
┡━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━┩
│ ENS00001       │ MAP1A         │
│ ENS00002       │ BIN1          │
│ ENS00003       │ ESR1          │
└────────────────┴───────────────┘

You can specify complex representations as columns, for example

obj = {
    "ensembl": ["ENS00001", "ENS00002", "ENS00002"],
    "symbol": ["MAP1A", "BIN1", "ESR1"],
    "ranges": BiocFrame({
        "chr": ["chr1", "chr2", "chr3"],
        "start": [1000, 1100, 5000],
        "end": [1100, 4000, 5500]
    }),
}

bframe2 = BiocFrame(obj, row_names=["row1", "row2", "row3"])
print(bframe2)

## output
BiocFrame with 3 rows & 3 columns
┏━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ row_names ┃ ensembl <list> ┃ symbol <list> ┃ ranges <BiocFrame>                          ┃
┡━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ row1      │ ENS00001       │ MAP1A         │ {'chr': 'chr1', 'start': 1000, 'end': 1100} │
│ row2      │ ENS00002       │ BIN1          │ {'chr': 'chr2', 'start': 1100, 'end': 4000} │
│ row3      │ ENS00002       │ ESR1          │ {'chr': 'chr3', 'start': 5000, 'end': 5500} │
└───────────┴────────────────┴───────────────┴─────────────────────────────────────────────┘

Properties

Properties can be accessed directly from the object, for e.g. column names, row names and/or dimensions of the BiocFrame.

# Dimensionality or shape
print(bframe.dims)

## output
## (3, 2)

# get the column names
print(bframe.column_names)

## output
## ['ensembl', 'symbol']

Setters

To set various properties

# set new column names
bframe.column_names = ["column1", "column2"]
print(bframe)

## output
BiocFrame with 3 rows & 2 columns
┏━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┓
┃ column1 <list> ┃ column2 <list> ┃
┡━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━┩
│ ENS00001       │ MAP1A          │
│ ENS00002       │ BIN1           │
│ ENS00003       │ ESR1           │
└────────────────┴────────────────┘

To add new columns,

bframe["score"] = range(2, 5)
print(bframe)

## output
BiocFrame with 3 rows & 3 columns
┏━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┓
┃ column1 <list> ┃ column2 <list> ┃ score <range> ┃
┡━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━┩
│ ENS00001       │ MAP1A          │ 2             │
│ ENS00002       │ BIN1           │ 3             │
│ ENS00003       │ ESR1           │ 4             │
└────────────────┴────────────────┴───────────────┘

Subset BiocFrame

Use the subset ([]) operator to slice the object,

sliced = bframe[1:2, [True, False, False]]
print(sliced)

## output
BiocFrame with 1 row & 1 column
┏━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┓
┃ row_names ┃ column1 <list> ┃
┡━━━━━━━━━━━╇━━━━━━━━━━━━━━━━┩
│ 1         │ ENS00002       │
└───────────┴────────────────┘

This operation accepts different slice input types, you can either specify a boolean vector, a slice object, a list of indices, or row/column names to subset.

Combine

BiocFrame implements the combine generic from biocgenerics. To combine multiple objects,

bframe1 = BiocFrame(
    {
        "odd": [1, 3, 5, 7, 9],
        "even": [0, 2, 4, 6, 8],
    }
)

bframe2 = BiocFrame(
    {
        "odd": [11, 33, 55, 77, 99],
        "even": [0, 22, 44, 66, 88],
    }
)

from biocgenerics.combine import combine
combined = combine(bframe1, bframe2)

# OR an object oriented approach

combined = bframe.combine(bframe2)

## output
BiocFrame with 10 rows & 2
        columns
┏━━━━━━━━━━━━┳━━━━━━━━━━━━━┓
┃ odd <list> ┃ even <list> ┃
┡━━━━━━━━━━━━╇━━━━━━━━━━━━━┩
│ 1          │ 0           │
│ 3          │ 2           │
│ ...        │ ...         │
│ 99         │ 88          │
└────────────┴─────────────┘

For more details, check out the BiocFrame class reference.

Note

This project has been set up using PyScaffold 4.5. For details and usage information on PyScaffold see https://pyscaffold.org/.