APR Detector

High-throughput pipeline for detecting A-phased repeats (APRs) in genomes with configurable spacing around the DNA helical pitch, symmetry-aware filtering, TpA dinucleotide handling, and multi-format export (TSV/GFF3/BED).

Authors

• Hamza Mohammed (mohammed-hamza@uiowa.edu; hamzamohammed1445@gmail.com), University of Iowa
• Josep Comeron, PhD (josep-comeron@uiowa.edu), University of Iowa

What it does

• Reads FASTA, cleans/validates sequences, and finds A/T-rich tracts.
• Chains tracts whose centers fall within pitch +/- spacing_window (pitch defaults to 10.5 bp, set with -p).
• Computes optional metrics per APR: mean spacing, spacing variance, and phase coherence (Q).
• Filters by tract count, spacing window, symmetry, TA policy, and optional metric thresholds.
• Exports TSV by default plus optional GFF3/BED; filenames use _APRs (for example Chr10_APRs.tsv or Chr10_20260101_120000_APRs.tsv).

Models (presets)

Model names are case-insensitive; suffixes only apply to Model1/Model2. Override any preset with flags.

• Model1: Homopolymer mode. Tracts may be pure A or pure T; APRs can mix them.
  • Model1a: Pure A only. TpA spacer filtering applies only in heteropolymer mode, so it has no effect here.
  • Model1b: Pure T only.
• Model2: Heteropolymer mode (A/T tracts; homopolymer runs included).
  • Model2a: Heteropolymer-only (drops pure A or pure T); TpA spacers allowed.
  • Model2b: Symmetry-focused heteropolymer (symmetry forced to only).
• Model3: Uses Cer et al., 2013 TpA-restart approach. Symmetry flags and suffixes are ignored; selecting Model3 is enough.

Model flow

flowchart TD
    A[Select model] --> M1[Model1]
    A --> M2[Model2]
    A --> M3[Model3]
    M1 --> M1a[Model1a]
    M1 --> M1b[Model1b]
    M2 --> M2a[Model2a]
    M2 --> M2b[Model2b]

    subgraph Standard[Standard APR pipeline]
        S1[Read and clean sequence] --> S2[Find A and T tracts]
        S2 --> S3[Apply symmetry mode]
        S3 --> S4[Group tracts into APRs]
        S4 --> S5[Compute metrics and export]
    end

    subgraph TAPath[Model 3 Pipeline]
        T1[Scan AT runs] --> T2[Find tract centers]
        T2 --> T3[Build APRs with fixed spacing]
        T3 --> T4[Export APRs]
    end

    M1 -->|homopolymer mixed| Standard
    M1a -->|A only tracts| Standard
    M1b -->|T only tracts| Standard
    M2 -->|heteropolymer| Standard
    M2a -->|mixed A and T only| Standard
    M2b -->|symmetry focused| Standard
    M3 -->TAPath

CLI flags (short)

-i       FASTA file (positional alternative: first argument)
-o       Output directory (positional alternative: second argument)
-l       Minimum tract length (default 4)
-t       Minimum tracts per APR (default 3; can be set as low as 2)
-w       Allowed deviation around pitch (default 0.5; min/max = pitch +/- window)
-p       Helical pitch in bp (default 10.5; used for spacing window and phase coherence)
-n       0=remove, 1=keep (default), 2=error
-y       1=include, 0=exclude, 2=only (ignored for Model3)
-m       1=merge overlapping/contained APRs (default), 0=keep separate
-ta      1=allow TA inside tracts (default), 0=reject such tracts
-csv     Also write APRs to CSV (optional path override)
-tracts  Write candidate tracts to CSV (pre-APR filtering; can be large)
-tracts-tsv  Write candidate tracts to TSV (pre-APR filtering; can be large)
-u       Optional max mean spacing filter (bp)
-v       Optional max spacing variance filter (bp^2)
-q       Optional min phase coherence filter (0-1)
-s       1=forward only (default), 2=both strands
-c       Worker count for multiprocessing (default 1)
-g       Also write GFF3
-b       Also write BED
-nt      Omit timestamps in filenames

Metrics (reported in TSV, used for optional filtering)

• Mean spacing (mu): Arithmetic mean of inter-tract center spacings.
• Spacing variance (sigma^2): Sample variance of the spacings (consistency of spacing). No default cutoff; set -v to filter.
• Phase coherence (Q): Q = 1 - r_bar / Rmax, where each residual r_i is the distance from a spacing to the nearest multiple of the pitch.
  • Rmax defaults to pitch/2 unless overridden in ScoringConfig.PHASE_RMAX.
  • A small epsilon protects division when residuals vanish; Q is clamped to [0,1].
  • Set -q to require a minimum phase coherence.

Spacing window & pitch

• Effective spacing bounds are pitch - spacing_window to pitch + spacing_window, echoed in logs and TSV headers.
• The window is not hard-coded to 10.5; adjust -p to shift the target pitch and -w to widen/narrow tolerance.

Outputs

• TSV (default): Parameter header on the first line with flag-style labels; columns include Mean_spacing, Spacing_variance, and Phase_Coherence.
• CSV (optional with -csv): Same APR content as TSV, comma-separated.
• GFF3 (optional): Feature type APR; attributes include tract count, tract sequences, composition, and metrics when available.
• BED6 (optional): Name APR_<n>, score equals tract count.
• Output stems use _APRs before the extension (for example _APRs.tsv, _APRs.gff, _APRs.bed).
• Tracts CSV/TSV (optional with -tracts and -tracts-tsv): All candidate tracts prior to APR spacing filters; includes positions, strand, sequence, symmetry flag, and mode settings. Warning: can be very large on whole genomes; consider per-chromosome runs, stricter tract settings (higher -l, symmetry-only, hetero-only), ample disk space, or compression.

Install (pip)

pip install apr-detector

CLI

apr-detector Model2 \
  -i /path/to/genome.fasta \
  -o output/ \
  -l 4 -t 3 -w 0.5 -p 10.5 \
  -c 8 -g -b

Quick start

python scripts/main.py Model2 \
  -i /path/to/genome.fasta \
  -o output/ \
  -l 4 -t 3 -w 0.5 -p 10.5 \
  -c 8 -g -b

Testing

python -m pip install -e .[test]
PYTEST_DISABLE_PLUGIN_AUTOLOAD=1 python -m pytest

Tests read tests/data/S_cerevisiae_chr1.fasta and use the first 20,000 bases by default. Set APR_TEST_MAX_BASES to control the prefix length (use 0 to read the full file).

Python version

Tested with Python 3.9-3.12.

Configuration notes

• Defaults live in apr_detector/config/config.py (APRConfig) and apr_detector/core/scoring.py (ScoringConfig); both validate on startup.
• Minimum tracts per APR default to 3; values below 2 are rejected (at least one spacing is required).
• Ambiguous handling affects tract discovery only.
• TA inside tracts is controlled with -ta; TpA spacer filtering applies only in heteropolymer mode.
• Case-insensitive model names allow flexible CLI input (for example model2b, MODEL1A).

Repository layout

• apr_detector/cli.py - CLI entry point; orchestrates ingestion, detection, and export.
• apr_detector/core/ - tract discovery (tract.py), APR grouping (detector.py), scoring (scoring.py), and utilities.
• apr_detector/config/config.py - central defaults and validation.
• scripts/main.py - source wrapper for local runs.
• output/ - example outputs for reference.

Support

• Hamza Mohammed - mohammed-hamza@uiowa.edu / hamzamohammed1445@gmail.com
• Josep Comeron, PhD - josep-comeron@uiowa.edu