snp2str 0.1

A Python tool for converting SNP genotype data in PED format to a format suitable for STRUCTURE analysis

SNP2STR

A Python tool for converting SNP genotype data in PED file (.ped) format to a format suitable for STRUCTURE analysis.

Overview

SNP2STR processes genomic data files, specifically PED files (.ped) containing SNP (Single Nucleotide Polymorphism) genotype data, and converts them into a format that can be used for population structure analysis with STRUCTURE software. The tool handles the conversion of nucleotide bases to numeric codes required by STRUCTURE.

Features

• Converts PED files (.ped) to STRUCTURE input format
• Supports optional POPULATION file (.txt) and MAP file (.map)
• Validates input data for consistency
• Handles nucleotide base coding conversion
• Provides command-line interface for easy usage
• Supports header customization in output files

Installation

# Install from PyPI
pip install snp2str

# Or clone the repository
git clone https://github.com/vladgheorghe/snp2str.git
cd snp2str
pip install -e .

Requirements

• Python 3.6+
• pandas 2.2.3

Usage

Command Line Interface

# Basic usage with a PED file (.ped)
snp2str path/to/your/file.ped

# Using all optional files
snp2str path/to/your/file.ped path/to/your/populations.txt path/to/your/file.map

# Specify output path
snp2str path/to/your/file.ped --output custom_output.csv

# Skip header in output file
snp2str path/to/your/file.ped --skip-output-header

# Skip first line in input PED file (.ped)
snp2str path/to/your/file.ped --skip-input-header

Python API

from snp2str.process import process_files

# Basic usage
process_files(ped_path="path/to/your/file.ped")

# With all options
process_files(
    ped_path="path/to/your/file.ped",
    pop_path="path/to/your/populations.txt",
    map_path="path/to/your/file.map",
    add_header=True,
    output_path="custom_output.csv",
    skip_input_header=False
)

Input Files

1. PED file (.ped) - Required

   • Contains genotype data with SNP information
   • Each row represents an individual
   • First 6 columns contain metadata, followed by genotype data

2. POPULATION file (.txt) - Optional

   • Contains population information for each individual
   • One population identifier per line

3. MAP file (.map) - Optional

   • Contains marker information
   • Used to generate headers in the output file

Output Format

The output is a CSV file formatted for STRUCTURE analysis:

• Each individual is represented by two rows (one for each chromosome)
• First column contains the individual identifier
• Second column contains the population identifier (if provided)
• Remaining columns contain the coded alleles

Base Coding

SNP bases are coded according to the following scheme:

• A → 1
• T → 2
• G → 3
• C → 4
• Missing data → -9