ferromic 0.1.2__cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl

ferromic/__init__.py

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+from .ferromic import *
+
+__doc__ = ferromic.__doc__
+if hasattr(ferromic, "__all__"):
+    __all__ = ferromic.__all__

ferromic-0.1.2.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: ferromic
+Version: 0.1.2
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: Other/Proprietary License
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Rust
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Dist: numpy>=1.23
+Requires-Dist: pytest ; extra == 'test'
+Requires-Dist: numpy ; extra == 'test'
+Requires-Dist: scikit-allel ; extra == 'test'
+Requires-Dist: scipy ; extra == 'test'
+Requires-Dist: pytest-benchmark ; extra == 'test'
+Requires-Dist: patchelf ; platform_system == 'Linux' and extra == 'test'
+Provides-Extra: test
+License-File: LICENSE.md
+Summary: Rust-accelerated population genetics toolkit with ergonomic Python bindings
+Keywords: population-genetics,bioinformatics,rust,pyo3,numpy
+Home-Page: https://github.com/SauersML/ferromic
+Author: SauersML
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+
+# Ferromic
+
+A Rust-based tool for population genetic analysis that calculates diversity statistics from VCF files, with support for haplotype-group-specific analyses and genomic regions.
+
+## Overview
+
+Ferromic processes genomic variant data from VCF files to calculate key population genetic statistics. It can analyze diversity metrics separately for different haplotype groups (0 and 1) as defined in a configuration file, making it particularly useful for analyzing regions with structural variants or any other genomic features where haplotypes can be classified into distinct groups.
+
+## Features
+
+- Efficient VCF processing using multi-threaded parallelization
+- Calculate key population genetic statistics:
+  - Nucleotide diversity (π)
+  - Watterson's theta (θ)
+  - Segregating sites counts
+  - Allele frequencies
+- Apply various filtering strategies:
+  - Genotype quality (GQ) thresholds
+  - Genomic masks (exclude regions)
+  - Allowed regions (include only)
+  - Multi-allelic site handling
+  - Missing data management
+- Extract coding sequences (CDS) from genomic regions using GTF annotations
+- Generate PHYLIP format sequence files for phylogenetic analysis
+- Create per-site diversity statistics for fine-grained analysis
+- Support both individual region analysis and batch processing via configuration files
+
+## Python bindings
+
+Ferromic's Rust core is exposed to Python through [PyO3](https://pyo3.rs) and
+is distributed as a binary wheel on PyPI. Installing the extension pulls in the
+compiled Rust library together with its runtime dependency on NumPy:
+
+```bash
+pip install ferromic
+```
+
+Once installed, the `ferromic` module mirrors the high-level statistics API of
+the Rust crate. The example below shows how to construct an in-memory
+population, compute basic diversity statistics, and run a principal component
+analysis directly from Python:
+
+```python
+import numpy as np
+import ferromic as fm
+
+genotypes = np.array([
+    [[0, 0], [0, 1], [1, 1]],
+    [[0, 1], [0, 0], [1, 1]],
+], dtype=np.uint8)
+
+population = fm.Population.from_numpy(
+    "demo",
+    genotypes=genotypes,
+    positions=[101, 202],  # plain Python sequences are accepted
+    haplotypes=[(0, 0), (0, 1), (1, 0), (1, 1), (2, 0), (2, 1)],
+    sequence_length=1000,
+    sample_names=["sampleA", "sampleB", "sampleC"],
+)
+
+print(f"Ferromic version: {fm.__version__}")
+print("Segregating sites:", population.segregating_sites())
+print("Nucleotide diversity:", population.nucleotide_diversity())
+
+pca = fm.chromosome_pca(
+    variants=[
+        {"position": 101, "genotypes": [[0, 0], [0, 1], [1, 1]]},
+        {"position": 202, "genotypes": [[0, 1], [0, 0], [1, 1]]},
+    ],
+    sample_names=["sampleA", "sampleB", "sampleC"],
+)
+
+print("PCA components shape:", pca.coordinates.shape)
+```
+
+Additional helpers for Hudson FST, Weir & Cockerham FST, sequence length
+adjustment, and inversion allele frequency are available under the top-level
+`ferromic` namespace. Consult `src/pytests` for further end-to-end examples
+and integration tests.
+
+## Usage
+
+```
+cargo run --release --bin run_vcf -- [OPTIONS]
+```
+
+### Required Arguments
+
+- `--vcf_folder <FOLDER>`: Directory containing VCF files
+- `--reference <PATH>`: Path to reference genome FASTA file
+- `--gtf <PATH>`: Path to GTF annotation file
+
+### Optional Arguments
+
+- `--chr <CHROMOSOME>`: Process a specific chromosome
+- `--region <START-END>`: Process a specific region (1-based coordinates)
+- `--config_file <FILE>`: Configuration file for batch processing multiple regions
+- `--output_file <FILE>`: Output file path (default: output.csv)
+- `--min_gq <INT>`: Minimum genotype quality threshold (default: 30)
+- `--mask_file <FILE>`: BED file of regions to exclude
+- `--allow_file <FILE>`: BED file of regions to include
+- `--pca`: Perform principal component analysis on filtered haplotypes (writes per-chromosome TSV files under `pca_per_chr_outputs/`)
+- `--pca_components <INT>`: Number of principal components to compute (default: 10)
+- `--pca_output <FILE>`: Desired filename for the combined PCA summary table produced by Ferromic's PCA utilities (default: `pca_results.tsv`)
+- `--fst`: Enable haplotype FST calculations (required for Weir & Cockerham and Hudson outputs)
+- `--fst_populations <FILE>`: Optional CSV (population name followed by comma-separated sample IDs) describing named populations for additional FST comparisons
+
+## Example Command
+
+```
+cargo run --release --bin run_vcf -- \
+    --vcf_folder ../vcfs \
+    --config_file ../variants.tsv \
+    --mask_file ../hardmask.bed \
+    --reference ../hg38.no_alt.fa \
+    --gtf ../hg38.knownGene.gtf
+```
+
+## Coordinate Systems
+
+Ferromic handles different coordinate systems:
+- VCF files: 1-based coordinates
+- BED mask/allow files: 0-based, half-open intervals
+- TSV config files: 1-based, inclusive coordinates
+- GTF files: 1-based, inclusive coordinates
+
+## Configuration File Format
+
+The configuration file must be tab-delimited. Ferromic expects the header to begin with seven metadata columns followed by one column per sample:
+
+1. `seqnames`: Chromosome (with or without "chr" prefix)
+2. `start`: Region start position (1-based, inclusive)
+3. `end`: Region end position (1-based, inclusive)
+4. `POS`: Representative variant position within the region (retained for bookkeeping)
+5. `orig_ID`: Region identifier
+6. `verdict`: Manual/automated review verdict
+7. `categ`: Category label for the region
+
+Columns eight onward must be sample names. Each cell in these sample columns stores a genotype string such as `"0|0"`, `"0|1"`, `"1|0"`, or `"1|1"` that assigns both haplotypes to group 0 or group 1.
+
+Where:
+- "0" and "1" represent the two haplotype groups to be analyzed separately
+- The "|" character indicates the phase separation between left and right haplotypes
+- Genotypes with special formats (e.g., "0|1_lowconf") are included in unfiltered analyses but excluded from filtered analyses
+
+## Output Files
+
+### Main CSV Output
+
+Contains summary statistics for each region with columns:
+```
+chr,region_start,region_end,0_sequence_length,1_sequence_length,
+0_sequence_length_adjusted,1_sequence_length_adjusted,
+0_segregating_sites,1_segregating_sites,0_w_theta,1_w_theta,
+0_pi,1_pi,0_segregating_sites_filtered,1_segregating_sites_filtered,
+0_w_theta_filtered,1_w_theta_filtered,0_pi_filtered,1_pi_filtered,
+0_num_hap_no_filter,1_num_hap_no_filter,0_num_hap_filter,1_num_hap_filter,
+inversion_freq_no_filter,inversion_freq_filter,
+haplotype_overall_fst_wc,haplotype_between_pop_variance_wc,
+haplotype_within_pop_variance_wc,haplotype_num_informative_sites_wc,
+hudson_fst_hap_group_0v1,hudson_dxy_hap_group_0v1,
+hudson_pi_hap_group_0,hudson_pi_hap_group_1,hudson_pi_avg_hap_group_0v1
+```
+
+Where:
+- Values prefixed with "0_" are statistics for haplotype group 0
+- Values prefixed with "1_" are statistics for haplotype group 1
+- "sequence_length" is the raw length of the region
+- "sequence_length_adjusted" accounts for masked regions
+- "num_hap" columns indicate the number of haplotypes in each group
+- Statistics with "_filtered" are calculated from strictly filtered data
+- Columns prefixed with `haplotype_` contain Weir & Cockerham FST outputs; they are
+  populated when haplotype FST analysis is enabled and `NA` when insufficient data
+  are available
+- Columns prefixed with `hudson_` summarise Hudson-style FST components for the
+  haplotype 0 vs. 1 comparison and are likewise `NA` when FST statistics cannot be
+  computed
+
+### Per-site FASTA-style outputs
+
+Two FASTA-like files are produced in the working directory to capture
+position-specific metrics:
+
+- `per_site_diversity_output.falsta` – per-haplotype π and θ values. Each record is
+  emitted with a FASTA-style header such as
+  `>filtered_pi_chr_X_start_Y_end_Z_group_0` followed by a comma-separated vector of
+  site-wise values (one entry per base in the region). `NA` marks positions without
+  data and `0` marks zero-valued statistics.
+- `per_site_fst_output.falsta` – per-site summaries for Weir & Cockerham and Hudson
+  FST. Headers identify the statistic (overall FST, pairwise 0 vs 1, or Hudson
+  haplotype FST) and the associated region, with comma-separated values mirroring the
+  region length.
+
+Both files encode positions implicitly by index: the first entry corresponds to the
+region start (1-based), the second to start + 1, and so on.
+
+### Hudson FST TSV (optional)
+
+When run with `--fst`, Ferromic writes `hudson_fst_results.tsv` alongside the main
+CSV. The TSV header is: `chr`, `region_start_0based`, `region_end_0based`,
+`pop1_id_type`, `pop1_id_name`, `pop2_id_type`, `pop2_id_name`, `Dxy`, `pi_pop1`,
+`pi_pop2`, `pi_xy_avg`, `FST`. Region coordinates are 0-based inclusive and the
+population columns capture the identifier type (haplotype group or named
+population) alongside the label for each comparison.
+
+### PHYLIP Files
+
+Generated for each transcript that overlaps with the query region:
+- File naming: `group_{0/1}_{transcript_id}_chr_{chromosome}_start_{start}_end_{end}_combined.phy`
+- Contains aligned sequences (based on the reference genome with variants applied)
+- Sample names in the PHYLIP files are constructed from sample names with "_L" or "_R" suffixes to indicate left or right haplotypes
+
+## Implementation Details
+
+- For PHYLIP files, if a CDS region overlaps with the query region (even partially), the entire transcript's coding sequence is included
+- For diversity statistics (π and θ), only variants strictly within the region boundaries are used
+- Different filtering approaches:
+  - Unfiltered: Includes all valid genotypes, regardless of quality or exact format
+  - Filtered: Excludes low-quality variants, masked regions, and non-standard genotypes
+- Sequence length is adjusted for masked regions when calculating diversity statistics
+- Multi-threading is implemented via Rayon for efficient processing
+- Missing data is properly accounted for in diversity calculations
+- Special values in results:
+  - θ = 0: No segregating sites (no genetic variation)
+  - θ = Infinity: Insufficient haplotypes or zero sequence length
+  - π = 0: No nucleotide differences (genetic uniformity)
+  - π = Infinity: Insufficient data
+
+## Python bindings with PyO3
+
+Ferromic now ships with a rich, Python-first API powered by
+[PyO3](https://pyo3.rs/). You can compute the same high-performance statistics
+that drive the Rust binaries directly from notebooks or scripts using familiar
+Python data structures.
+
+### Building the extension module
+
+1. Install Python 3.8+ and the [maturin](https://github.com/PyO3/maturin) build tool
+   (include the optional `patchelf` dependency on Linux to enable rpath fixing):
+   ```bash
+   python -m pip install "maturin[patchelf]"
+   ```
+2. Compile and install the extension into your active virtual environment:
+   ```bash
+   maturin develop --release
+   ```
+   The command compiles the `ferromic` shared library and makes it importable from Python. To
+   target a specific interpreter (for example, one provided by Conda), pass
+   `--python /path/to/python` or set the `PYO3_PYTHON` environment variable before invoking
+   `maturin`.
+
+After `maturin develop` completes successfully, you can import the module with `import ferromic`
+inside Python.
+
+### Ergonomic Python API
+
+All functions accept plain Python collections. Variants can be dictionaries,
+dataclasses, namedtuples or any object exposing a ``position`` attribute and a
+``genotypes`` iterable (with allele integers or ``None``). Haplotype entries are
+interpreted from tuples like ``(sample_index, "L")`` or ``(sample_index, 1)``.
+
+| Function or class | Description |
+| --- | --- |
+| `ferromic.segregating_sites(variants)` | Count polymorphic sites. |
+| `ferromic.nucleotide_diversity(variants, haplotypes, sequence_length)` | Compute π (nucleotide diversity). |
+| `ferromic.watterson_theta(segregating_sites, sample_count, sequence_length)` | Watterson's θ estimator. |
+| `ferromic.pairwise_differences(variants, sample_count)` | List of `PairwiseDifference` objects containing counts for every sample pair. |
+| `ferromic.per_site_diversity(variants, haplotypes, region=None)` | Per-position π and θ as `DiversitySite` objects. |
+| `ferromic.Population` | Reusable container for Hudson-style statistics. Pass either a haplotype group (0/1) or a custom label. |
+| `ferromic.hudson_dxy(pop1, pop2)` | Between-population nucleotide diversity. |
+| `ferromic.hudson_fst(pop1, pop2)` | Hudson FST with rich metadata. |
+| `ferromic.hudson_fst_sites(pop1, pop2, region)` | Per-site Hudson components across a region. |
+| `ferromic.hudson_fst_with_sites(pop1, pop2, region)` | Tuple ``(HudsonFstResult, [HudsonFstSite, ...])``. |
+| `ferromic.wc_fst(variants, sample_names, sample_to_group, region)` | Weir & Cockerham FST with pairwise and per-site summaries. |
+| `ferromic.wc_fst_components(fst_estimate)` | Extract `(value, sum_a, sum_b, sites)` from any `FstEstimate`. |
+| `ferromic.chromosome_pca(variants, sample_names, n_components=10)` | Run PCA for a single chromosome and return a `ChromosomePcaResult`. |
+| `ferromic.chromosome_pca_to_file(variants, sample_names, chromosome, output_dir, n_components=10)` | Convenience helper that writes a TSV with PCA coordinates for one chromosome. |
+| `ferromic.per_chromosome_pca(variants_by_chromosome, sample_names, output_dir, n_components=10)` | Batch PCA analysis across chromosomes, emitting one TSV per chromosome. |
+| `ferromic.global_pca(variants_by_chromosome, sample_names, output_dir, n_components=10)` | Memory-efficient pipeline that runs per-chromosome PCA and produces a combined summary table. |
+| `ferromic.ChromosomePcaResult` | Light-weight container exposing `haplotype_labels`, `coordinates`, and `positions`. |
+| `ferromic.adjusted_sequence_length(start, end, allow=None, mask=None)` | Apply BED-style masks to a region length. |
+| `ferromic.inversion_allele_frequency(sample_map)` | Frequency of allele ``1`` across haplotypes. |
+
+Every result type is a tiny Python class with descriptive attributes and a
+readable ``repr`` making it pleasant to explore interactively.
+
+### End-to-end example
+
+```python
+from dataclasses import dataclass
+
+import ferromic
+
+
+@dataclass
+class Variant:
+    # Positions are zero-based and inclusive to match Ferromic's internal representation.
+    position: int
+    genotypes: list
+
+
+variants = [
+    Variant(position=999, genotypes=[(0, 0), (0, 1), None]),
+    Variant(position=1_009, genotypes=[(0, 0), (0, 0), (1, 1)]),
+]
+
+haplotypes = [(0, "L"), (0, "R"), (1, 0), (1, 1), (2, "L")]
+
+pi = ferromic.nucleotide_diversity(variants, haplotypes, sequence_length=100)
+theta = ferromic.watterson_theta(ferromic.segregating_sites(variants), len(haplotypes), 100)
+
+group0 = ferromic.Population(0, variants, haplotypes, sequence_length=100)
+group1 = ferromic.Population("inversion", variants, haplotypes, sequence_length=100)
+
+hudson = ferromic.hudson_fst(group0, group1)
+sites = ferromic.hudson_fst_sites(group0, group1, region=(990, 1_020))
+
+wc = ferromic.wc_fst(
+    variants,
+    sample_names=["S0", "S1", "S2"],
+    sample_to_group={"S0": (0, 0), "S1": (0, 1), "S2": (1, 1)},
+    region=(990, 1_020),
+)
+
+pca_result = ferromic.chromosome_pca(variants, ["S0", "S1", "S2"], n_components=3)
+ferromic.chromosome_pca_to_file(variants, ["S0", "S1", "S2"], "2L", "./pca_outputs")
+
+print(f"π={pi:.6f}, θ={theta:.6f}")
+print(hudson)
+print(sites[0])
+print(wc.overall_fst)
+print(pca_result.coordinates[0][:3])
+```
+
+The example demonstrates how the Python API mirrors Ferromic's Rust types while
+remaining easy to use from high-level workflows. Variants and haplotypes can be
+assembled from pandas data frames, NumPy arrays, or plain Python lists—Ferromic
+only inspects the fields it needs.
+
+

ferromic-0.1.2.dist-info/RECORD

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+ferromic-0.1.2.dist-info/licenses/LICENSE.md,sha256=ZUhjdsYcsoc7ZisJORA4kRd2t3eKONA_vPDeIqiRNFY,169
+ferromic/__init__.py,sha256=aNX1Ggsg2XdYFZ-hNIAQzCzjz7dGwk9BCdmrwwYZKh0,115
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ferromic-0.1.2.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: maturin (1.9.4)
+Root-Is-Purelib: false
+Tag: cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le

ferromic-0.1.2.dist-info/licenses/LICENSE.md

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+Copyright (c) 2025 Ferromic Developers. All rights reserved.
+
+Unauthorized copying of this project, via any medium is strictly prohibited.
+Proprietary and confidential.