ibdf 0.1.0b0

Python reader for IBDF v3 genomic pair files

ibdf-parser

ibdf-parser is a Python package for reading the Identity-by-Descent Binary Format (IBDF v3).

It reconstructs genomic identity-by-descent (IBD) segment sharing spans from delta and checkpoint blocks on the fly, supports fast bounded-replay random seeking, and automatically resolves numeric sample IDs back to their string names using companion .samples files.

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Installation

This package is managed using uv. To install it in editable development mode in your virtual environment:

uv pip install -e .

To run the test suite:

uv run pytest

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Core Features

• Drop-in standard file-like interface (ibdf.open): Behaves like Python's built-in gzip.open and standard file handlers. You can read lines, use it in for loops, or read byte chunks.
• Direct structural parsing (ibdf.IbdfFile): Allows users to iterate directly over Python dataclasses or string TSV encoding/decoding overhead for versatility.
• Genomic random access (seek_position / seek_index): Allows binary-searching the index to seek directly to a target chromosome position or block index by replaying from the nearest prior checkpoint.
• Breakpoint-by-breakpoint iteration (iter_breakpoints): Streams the chromosome position by position, yielding the active sharing segments at each physical breakpoint.

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API Reference

ibdf.open(filename, mode='rt', sample_file=None)

Opens an IBDF file and returns an IbdfFile instance configured in either file-like streaming mode or structured segment parsing mode.

• filename (str | Path): Path to the .ibdf binary file.
• mode (str): Open mode. Either 'r' / 'rt' (text mode, default), 'rb' (binary mode), or 'segments' (to iterate directly over IbdSegment NamedTuple objects).
• sample_file (str | Path | None): Optional path to a plain-text companion .samples file. If omitted, the reader will look for a companion file in the same directory (e.g., data.samples for data.ibdf). If found, it translates indices to sample names; otherwise, it defaults to using stringified numeric IDs.

ibdf.IbdSegment

A read-only dataclass representing a reconstructed IBD segment:

• sample1 (str | int): Name or ID of the first sample.
• sample2 (str | int): Name or ID of the second sample (always guaranteed that sample1 < sample2 lexicographically or numerically).
• start_bp (int): Genomic start position (base-pairs) of segment sharing.
• end_bp (int): Genomic end position (base-pairs) of segment sharing.
• cm (float): Genetic length of the segment in centiMorgans.

Properties & Methods on the Opened Handle (IbdfFile)

• read(size=-1): Read at most size characters/bytes.
• readline(): Read a single line.
• seek(0): Reset the reader to the beginning of the file.
• seek_position(bp_pos): Seek to the block at or immediately before the base-pair position bp_pos.
• seek_index(index): Seek to the block at the given position index index.
• positions (property: list[int]): List of all genomic breakpoint positions stored in the file.
• current_position (property: int | None): The base-pair position of the next block to be parsed.
• iter_breakpoints(): Yield (bp_pos, active_segments) sequentially for every breakpoint.

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Usage Examples

1. Drop-In Flat TSV Reading (Text Mode)

Iterating over the opened file handle yields lines formatted as standard tab-separated values: {sample1}\t{sample2}\t{start_bp}\t{end_bp}\t{cm:.6f}\n

import ibdf

# Automatically finds 'data.samples' in the same folder if present
with ibdf.open("data.ibdf", "r") as f:
    for line in f:
        sample1, sample2, start, end, cm = line.strip().split("\t")
        print(f"{sample1} shares IBD with {sample2} from {start} to {end} ({cm} cM)")

2. High-Performance Direct Dataclass Parsing

Bypass formatting strings to TSV and parsing them back by iterating directly over IbdSegment dataclasses.

import ibdf

# Open the parser directly
parser = ibdf.IbdfFile("data.ibdf")

# (Optional) Load sample names manually if they are not in a standard companion path
parser.sample_names = ["S0", "S1", "S2", "S3"]

# Yields structured IbdSegment objects
for segment in parser.iter_segments():
    print(segment.sample1, segment.sample2, segment.start_bp, segment.end_bp, segment.cm)

parser.close()

3. Bounded-Replay Genomic Seeking

Seek to any location on the chromosome without parsing the entire file from the beginning.

import ibdf

with ibdf.open("data.ibdf", "r") as f:
    # Seek directly to breakpoint at/before 12,500,000 base-pairs
    # This automatically loads the nearest checkpoint and replays deltas
    f.seek_position(12500000)
    
    print(f"Parser position: {f.current_position}")
    
    # Continue reading from the target position
    for line in f:
        print(line.strip())

4. Step Breakpoint-by-Breakpoint

Inspect the active sharing pairs at each physical breakpoint.

import ibdf

with ibdf.open("data.ibdf", "r") as f:
    for bp_pos, active_segments in f.iter_breakpoints():
        # bp_pos is the current breakpoint genomic coordinate
        # active_segments is a list of IbdSegment objects
        print(f"At breakpoint {bp_pos}, there are {len(active_segments)} active segments:")
        for segment in active_segments:
            print(f"  - Pair {segment.sample1} & {segment.sample2} started sharing at {segment.start_bp} ({segment.cm:.2f} cM)")