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/.