bio-wrangler

Bio-Wrangler

Bio-Wrangler is a bioinformatics data wrangling package for handling FASTA, FASTQ, VCF, and GFF files. It helps load, filter, merge, and summarize biological datasets in an easy and efficient manner.

Features

• Load FASTA, FASTQ, VCF, and GFF files into pandas DataFrames.
• Filter data by quality, chromosome, position, and specific attributes.
• Merge and summarize datasets.
• Save data to CSV or Excel formats.

Installation

You can install Bio-Wrangler directly from PyPI:

pip install bio-wrangler

Usage

Here’s how to use Bio-Wrangler to load, filter, and manipulate your bioinformatics datasets.

Loading Data

You can load data from FASTA, FASTQ, VCF, and GFF formats into pandas DataFrames for easy manipulation.

Example: Loading FASTA, FASTQ, VCF, and GFF Files

from bio_wrangler.bio_wrangler import BioWrangler

Initialize the BioWrangler class

wrangler = BioWrangler()

Load data from different formats

fasta_data = wrangler.load_fasta('path/to/sample.fasta') fastq_data = wrangler.load_fastq('path/to/sample.fastq') vcf_data = wrangler.load_vcf('path/to/sample.vcf') gff_data = wrangler.load_gff('path/to/sample.gff')

Display the first few rows of the datasets

print(fasta_data.head()) print(fastq_data.head()) print(vcf_data.head()) print(gff_data.head())

Filtering Data

You can filter the data by quality, chromosome, position, or specific attributes.

Example: Filtering FASTQ by Quality

filtered_fastq = wrangler.filter_fastq_by_quality(fastq_data, 30.0) print(filtered_fastq.head()) # Display FASTQ sequences with avg quality >= 30

Example: Filtering VCF by Chromosome and Position Range

filtered_vcf_by_chr = wrangler.filter_by_chromosome(vcf_data, 'chr1') filtered_vcf_by_pos = wrangler.filter_by_position_range(vcf_data, 100000, 500000)

print(filtered_vcf_by_chr.head()) print(filtered_vcf_by_pos.head())

Example: Filtering GFF by Attribute

filtered_gff = wrangler.filter_by_attribute(gff_data, 'ID', 'gene1') print(filtered_gff.head()) # Filter by gene ID

Summarizing Data

Generate a summary of the dataset, including total rows, average quality, and positional statistics.

Example: Summarizing FASTQ and VCF Data

fastq_summary = wrangler.summarize_fastq(fastq_data) vcf_summary = wrangler.summarize_data(vcf_data)

print(fastq_summary) print(vcf_summary)

Merging Datasets

Merge multiple datasets (e.g., two VCF datasets) into one for combined analysis.

Example: Merging VCF Datasets

merged_vcf = wrangler.merge_datasets(vcf_data, filtered_vcf_by_chr) print(merged_vcf.head()) # Combined dataset

Saving Data

You can save your processed data to a file in either CSV or Excel format.

Example: Saving Filtered VCF Data to a CSV File

wrangler.save_data(filtered_vcf_by_chr, 'filtered_vcf_output.csv', 'csv')

License

This project is licensed under the MIT License.