pyrsx 0.1.0

Python bindings for rsx: high-performance RAD-seq sex determination toolkit

pyrsx

Python bindings for rsx: a high-performance streaming toolkit for RAD-seq sex determination.

Installation

pip install pyrsx

Usage

import pyrsx

# Process FASTQ files into marker depth table
pyrsx.process("reads/", "markers.tsv", threads=4, min_depth=5)

# Compute distribution with Fisher's exact test + FDR
pyrsx.distrib("markers.tsv", "popmap.tsv", "distrib.tsv",
              test="fisher", correction="fdr")

# Extract significant markers with Bayesian output
pyrsx.signif("markers.tsv", "popmap.tsv", "signif.tsv",
             test="fisher", correction="fdr", bayes=True)

# Streaming PCA
pyrsx.pca("markers.tsv", "pca_results/", n_components=10)

# Merge tables (bounded memory, handles 75M+ sequences)
pyrsx.merge(["table1.tsv", "table2.tsv"], "merged.tsv")

Features

• All rsx commands accessible from Python
• 2-5x faster than C++ RADSex
• Bounded-memory streaming for arbitrarily large datasets
• Multiple statistical tests: chi-squared, Fisher's exact, G-test
• Multiple corrections: Bonferroni, Benjamini-Hochberg FDR
• Bayesian sex-linkage classification (Bayes Factor + posterior)
• Streaming PCA via Tucker mode-2 decomposition
• K-mer based marker deduplication