Bioconductor-like data frames

Overview

This package implements the BiocFrame class, a Bioconductor-friendly alternative to Pandas DataFrame. The main advantage is that the BiocFrame makes no assumption on the types of the columns - as long as an object has a length (__len__) and slicing methods (__getitem__), it can be used inside a BiocFrame. This allows us to accept arbitrarily complex objects as columns, which is often the case in Bioconductor objects.

To get started, install the package from PyPI:

pip install biocframe

# To install optional dependencies
pip install biocframe[optional]

Quick Examples

Genomic Annotation Data

Genomic data often requires storing coordinates, annotations, and metadata together:

# Gene annotation with nested structures
gene_annotations = BiocFrame({
    "gene_id": ["GENE1", "GENE2", "GENE3"],
    "symbol": ["BRCA1", "TP53", "EGFR"],
    "location": BiocFrame({
        "chromosome": ["chr17", "chr17", "chr7"],
        "start": [43044295, 7668422, 55019017],
        "end": [43125483, 7687550, 55211628],
        "strand": ["-", "-", "+"],
    }),
    "transcripts": [
        ["NM_007294", "NM_007297", "NM_007300"],
        ["NM_000546"],
        ["NM_005228", "NM_201282"],
    ],
    "pathways": [
        ["DNA repair", "Cell cycle"],
        ["Apoptosis", "Cell cycle", "DNA repair"],
        ["Cell growth", "Signal transduction"],
    ],
}, row_names=["ENSG00000012048", "ENSG00000141510", "ENSG00000146648"])

print(gene_annotations)

Multi-Omics Data Integration

When combining different types of omics data with varying structures:

# Multi-omics data with different measurement types
multi_omics = BiocFrame({
    "sample_id": ["S1", "S2", "S3"],
    "rna_seq": np.array([
        [100, 200, 150],
        [300, 250, 180],
        [120, 220, 160],
    ], dtype=np.float32),
    "methylation": BiocFrame({
        "cg0001": [0.85, 0.92, 0.78],
        "cg0002": [0.45, 0.38, 0.52],
        "cg0003": [0.12, 0.15, 0.10],
    }),
    "clinical": BiocFrame({
        "age": [45, 52, 38],
        "gender": ["M", "F", "F"],
        "diagnosis": ["Type A", "Type B", "Type A"],
    }),
}, column_data=BiocFrame({
    "data_type": ["identifier", "expression", "epigenetic", "clinical"],
    "source": ["lab", "sequencer", "array", "EHR"],
}))

print(multi_omics)
print("\nColumn metadata:")
print(multi_omics.get_column_data())

Hierarchical Data Structures

For data with natural hierarchies (e.g., samples → patients → cohorts):

# Hierarchical clinical trial data
clinical_trial = BiocFrame({
    "patient_id": ["P001", "P002", "P003"],
    "cohort": ["A", "A", "B"],
    "samples": [
        BiocFrame({
            "sample_id": ["S001", "S002"],
            "collection_date": ["2024-01-01", "2024-01-15"],
            "vital_status": ["alive", "alive"],
        }),
        BiocFrame({
            "sample_id": ["S003", "S004", "S005"],
            "collection_date": ["2024-01-02", "2024-01-16", "2024-01-30"],
            "vital_status": ["alive", "alive", "deceased"],
        }),
        BiocFrame({
            "sample_id": ["S006"],
            "collection_date": ["2024-01-03"],
            "vital_status": ["alive"],
        }),
    ],
}, metadata={
    "trial_name": "PHASE_III_STUDY",
    "start_date": "2024-01-01",
    "status": "ongoing",
})

print(clinical_trial)

Construction

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

from biocframe import BiocFrame

obj = {
    "ensembl": ["ENS00001", "ENS00002", "ENS00003"],
    "symbol": ["MAP1A", "BIN1", "ESR1"],
}
bframe = BiocFrame(obj)
print(bframe)
## BiocFrame with 3 rows and 2 columns
##      ensembl symbol
##       <list> <list>
## [0] ENS00001  MAP1A
## [1] ENS00002   BIN1
## [2] ENS00003   ESR1

You can specify complex objects as columns, as long as they have some "length" equal to the number of rows. For example, we can nest a BiocFrame inside another BiocFrame:

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)
## BiocFrame with 3 rows and 3 columns
##       ensembl symbol         ranges
##        <list> <list>    <BiocFrame>
## row1 ENS00001  MAP1A chr1:1000:1100
## row2 ENS00002   BIN1 chr2:1100:4000
## row3 ENS00002   ESR1 chr3:5000:5500

Extracting data

Properties can be accessed directly from the object:

print(bframe.shape)
## (3, 2)

print(bframe.get_column_names())
## ['ensembl', 'symbol']

print(bframe.column_names) # same as above
## ['ensembl', 'symbol']

We can fetch individual columns:

bframe.get_column("ensembl")
## ['ENS00001', 'ENS00002', 'ENS00003']

bframe["ensembl"]
## ['ENS00001', 'ENS00002', 'ENS00003']

And we can get individual rows as a dictionary:

bframe.get_row(2)
## {'ensembl': 'ENS00003', 'symbol': 'ESR1'}

To extract a subset of the data in the BiocFrame, we use the subset ([]) operator. This accepts different subsetting arguments like a boolean vector, a slice object, a sequence of indices, or row/column names.

sliced = bframe[1:2, [True, False, False]]
print(sliced)
## BiocFrame with 1 row and 1 column
##      column1
##       <list>
## [0] ENS00002

sliced = bframe[[0,2], ["symbol", "ensembl"]]
print(sliced)
## BiocFrame with 2 rows and 2 columns
##     symbol  ensembl
##     <list>   <list>
## [0]  MAP1A ENS00001
## [1]   ESR1 ENS00003

# Short-hand to get a single column:
bframe["ensembl"]
## ['ENS00001', 'ENS00002', 'ENS00003']

Setting data

Preferred approach

To set BiocFrame properties, we encourage a functional style of programming that avoids mutating the object. This avoids inadvertent modification of BiocFrames that are part of larger data structures.

modified = bframe.set_column_names(["column1", "column2"])
print(modified)
## BiocFrame with 3 rows and 2 columns
##      column1 column2
##       <list>  <list>
## [0] ENS00001   MAP1A
## [1] ENS00002    BIN1
## [2] ENS00003    ESR1

# Original is unchanged:
print(bframe.get_column_names())
## ['ensembl', 'symbol']

To add new columns, or replace existing columns:

modified = bframe.set_column("symbol", ["A", "B", "C"])
print(modified)
## BiocFrame with 3 rows and 2 columns
##      ensembl symbol
##       <list> <list>
## [0] ENS00001      A
## [1] ENS00002      B
## [2] ENS00003      C

modified = bframe.set_column("new_col_name", range(2, 5))
print(modified)
## BiocFrame with 3 rows and 3 columns
##      ensembl symbol new_col_name
##       <list> <list>      <range>
## [0] ENS00001  MAP1A            2
## [1] ENS00002   BIN1            3
## [2] ENS00003   ESR1            4

Change the row or column names:

modified = bframe.\
    set_column_names(["FOO", "BAR"]).\
    set_row_names(['alpha', 'bravo', 'charlie'])
print(modified)
## BiocFrame with 3 rows and 2 columns
##              FOO    BAR
##           <list> <list>
##   alpha ENS00001  MAP1A
##   bravo ENS00002   BIN1
## charlie ENS00003   ESR1

We also support Bioconductor's metadata concepts, either along the columns or for the entire object:

modified = bframe.\
    set_metadata({ "author": "Jayaram Kancherla" }).\
    set_column_data(BiocFrame({"column_source": ["Ensembl", "HGNC" ]}))
print(modified)
## BiocFrame with 3 rows and 2 columns
##      ensembl symbol
##       <list> <list>
## [0] ENS00001  MAP1A
## [1] ENS00002   BIN1
## [2] ENS00003   ESR1
## ------
## column_data(1): column_source
## metadata(1): author

The other way

Properties can also be set by direct assignment for in-place modification. We prefer not to do it this way as it can silently mutate BiocFrame instances inside other data structures. Nonetheless:

testframe = BiocFrame({ "A": [1,2,3], "B": [4,5,6] })
testframe.column_names = ["column1", "column2" ]
print(testframe)
## BiocFrame with 3 rows and 2 columns
##     column1 column2
##      <list>  <list>
## [0]       1       4
## [1]       2       5
## [2]       3       6

Similarly, we could set or replace columns directly:

testframe["column2"] = ["A", "B", "C"]
testframe[1:3, ["column1","column2"]] = BiocFrame({"x":[4, 5], "y":["E", "F"]})
## BiocFrame with 3 rows and 2 columns
##     column1 column2
##      <list>  <list>
## [0]       1       A
## [1]       4       E
## [2]       5       F

These assignments are the same as calling the corresponding set_*() methods with in_place = True. It is best to do this only if the BiocFrame object is not being used anywhere else; otherwise, it is safer to just create a (shallow) copy via the default in_place = False.

Combining objects

BiocFrame implements methods for the various combine generics from BiocUtils. So, for example, to combine by row:

import biocutils

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],
    }
)

combined = biocutils.combine_rows(bframe1, bframe2)
print(combined)
## BiocFrame with 10 rows and 2 columns
##        odd   even
##     <list> <list>
## [0]      1      0
## [1]      3      2
## [2]      5      4
## [3]      7      6
## [4]      9      8
## [5]     11      0
## [6]     33     22
## [7]     55     44
## [8]     77     66
## [9]     99     88

Similarly, to combine by column:

bframe3 = BiocFrame(
    {
        "foo": ["A", "B", "C", "D", "E"],
        "bar": [True, False, True, False, True]
    }
)

combined = biocutils.combine_columns(bframe1, bframe3)
print(combined)
BiocFrame with 5 rows and 4 columns
       odd   even    foo    bar
    <list> <list> <list> <list>
[0]      1      0      A   True
[1]      3      2      B  False
[2]      5      4      C   True
[3]      7      6      D  False
[4]      9      8      E   True

By default, both methods above assume that the number and identity of columns (for combine_rows()) or rows (for combine_columns()) are the same across objects. If this is not the case, e.g., with different columns across objects, we can use BiocFrame's relaxed_combine_rows() instead:

from biocframe import relaxed_combine_rows
modified2 = bframe2.set_column("foo", ["A", "B", "C", "D", "E"])
combined = relaxed_combine_rows(bframe1, modified2)
print(combined)
## BiocFrame with 10 rows and 3 columns
##        odd   even    foo
##     <list> <list> <list>
## [0]      1      0   None
## [1]      3      2   None
## [2]      5      4   None
## [3]      7      6   None
## [4]      9      8   None
## [5]     11      0      A
## [6]     33     22      B
## [7]     55     44      C
## [8]     77     66      D
## [9]     99     88      E

Similarly, if the rows are different, we can use BiocFrame's merge function:

from biocframe import merge
modified1 = bframe1.set_row_names(["A", "B", "C", "D", "E"])
modified3 = bframe3.set_row_names(["C", "D", "E", "F", "G"])
combined = merge([modified1, modified3], by=None, join="outer")
## BiocFrame with 7 rows and 4 columns
##      odd   even    foo    bar
##   <list> <list> <list> <list>
## A      1      0   None   None
## B      3      2   None   None
## C      5      4      A   True
## D      7      6      B  False
## E      9      8      C   True
## F   None   None      D  False
## G   None   None      E   True

Playing nice with pandas

BiocFrame is intended for accurate representation of Bioconductor objects for interoperability with R. Most users will probably prefer to work with pandas DataFrame objects for their actual analyses. This conversion is easily achieved:

from biocframe import BiocFrame
bframe = BiocFrame(
    {
        "foo": ["A", "B", "C", "D", "E"],
        "bar": [True, False, True, False, True]
    }
)

pd = bframe.to_pandas()
print(pd)
##   foo    bar
## 0   A   True
## 1   B  False
## 2   C   True
## 3   D  False
## 4   E   True

Conversion back to a BiocFrame is similarly easy:

out = BiocFrame.from_pandas(pd)
print(out)
## BiocFrame with 5 rows and 2 columns
##      foo    bar
##   <list> <list>
## 0      A   True
## 1      B  False
## 2      C   True
## 3      D  False
## 4      E   True

Further reading

Check out the reference documentation for more details.

Also see check out Bioconductor's S4Vectors package, which implements the DFrame class on which BiocFrame was based.