{"id":21634335,"url":"https://github.com/se7en69/bio-wrangler","last_synced_at":"2026-02-06T09:05:33.457Z","repository":{"id":262499536,"uuid":"869962374","full_name":"se7en69/bio-wrangler","owner":"se7en69","description":"Bio-Wrangler is a Python package for bioinformatics data wrangling. 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The package allows users to load, filter, summarize, and merge bioinformatics datasets into pandas DataFrames, enabling efficient data manipulation and analysis.\r\n\r\n## Features\r\n\r\n- Load **FASTA**, **FASTQ**, **VCF**, and **GFF** files into pandas DataFrames.\r\n- Filter data based on quality, chromosome, position, and attributes.\r\n- Summarize datasets to extract key statistics.\r\n- Merge multiple datasets.\r\n- Save processed data to CSV or Excel formats.\r\n\r\n## Table of Contents\r\n- [Installation](#installation)\r\n- [Usage](#usage)\r\n  - [Loading Data](#loading-data)\r\n  - [Filtering Data](#filtering-data)\r\n  - [Summarizing Data](#summarizing-data)\r\n  - [Merging Datasets](#merging-datasets)\r\n  - [Saving Data](#saving-data)\r\n- [Contributing](#contributing)\r\n- [License](#license)\r\n\r\n## Installation\r\n\r\nTo install Bio-Wrangler, use the following command:\r\n\r\npip install bio-wrangler\r\n\r\n\r\n## Usage\r\n\r\n### 1. Loading Data\r\n\r\nBio-Wrangler provides methods to load bioinformatics files into pandas DataFrames.\r\n\r\n#### Example: Loading FASTA, FASTQ, VCF, and GFF Files\r\n\r\nfrom bio_wrangler.bio_wrangler import BioWrangler\r\n\r\n# Initialize the class\r\nwrangler = BioWrangler()\r\n\r\n# Load a FASTA file\r\nfasta_data = wrangler.load_fasta('path/to/sample.fasta')\r\nprint(fasta_data.head())\r\n\r\n# Load a FASTQ file\r\nfastq_data = wrangler.load_fastq('path/to/sample.fastq')\r\nprint(fastq_data.head())\r\n\r\n# Load a VCF file\r\nvcf_data = wrangler.load_vcf('path/to/sample.vcf')\r\nprint(vcf_data.head())\r\n\r\n# Load a GFF file\r\ngff_data = wrangler.load_gff('path/to/sample.gff')\r\nprint(gff_data.head())\r\n\r\n\r\n### 2. Filtering Data\r\n\r\nBio-Wrangler allows you to filter data based on various criteria such as quality, chromosome, position, and attributes.\r\n\r\n#### Example: Filtering FASTQ by Quality\r\n\r\n# Filter FASTQ data by average quality score threshold\r\nfiltered_fastq = wrangler.filter_fastq_by_quality(fastq_data, 30.0)\r\nprint(filtered_fastq.head())\r\n\r\n#### Example: Filtering VCF by Chromosome\r\n\r\n# Filter VCF data to retain only records from a specific chromosome\r\nfiltered_vcf = wrangler.filter_by_chromosome(vcf_data, 'chr1')\r\nprint(filtered_vcf.head())\r\n\r\n\r\n#### Example: Filtering GFF by Attribute\r\n\r\n# Filter GFF data by a specific attribute, such as gene_id\r\nfiltered_gff = wrangler.filter_by_attribute(gff_data, 'ID', 'gene1')\r\nprint(filtered_gff.head())\r\n\r\n\r\n#### Example: Filtering VCF by Position Range\r\n\r\n# Filter VCF data by a specific position range\r\nfiltered_vcf_range = wrangler.filter_by_position_range(vcf_data, 100000, 500000)\r\nprint(filtered_vcf_range.head())\r\n\r\n\r\n### 3. Summarizing Data\r\n\r\nBio-Wrangler can generate summary statistics for your datasets.\r\n\r\n#### Example: Summarizing FASTQ Data\r\n\r\n# Summarize FASTQ data\r\nfastq_summary = wrangler.summarize_fastq(fastq_data)\r\nprint(fastq_summary)\r\n\r\n\r\n#### Example: Summarizing VCF Data\r\n\r\n# Summarize VCF data\r\nvcf_summary = wrangler.summarize_data(vcf_data)\r\nprint(vcf_summary)\r\n\r\n\r\n### 4. Merging Datasets\r\n\r\nBio-Wrangler can merge multiple datasets into a single DataFrame.\r\n\r\n#### Example: Merging VCF Datasets\r\n\r\n\r\n# Merge two VCF datasets\r\nmerged_vcf = wrangler.merge_datasets(vcf_data, filtered_vcf)\r\nprint(merged_vcf.head())\r\n\r\n\r\n### 5. Saving Data\r\n\r\nAfter processing your data, you can save it to CSV or Excel formats using Bio-Wrangler.\r\n\r\n#### Example: Saving Filtered VCF Data to CSV\r\n\r\n# Save the filtered VCF data to a CSV file\r\nwrangler.save_data(filtered_vcf, 'filtered_vcf_output.csv', 'csv')\r\n\r\n\r\n#### Example: Saving Data to Excel\r\n\r\n# Save data to an Excel file\r\nwrangler.save_data(filtered_fastq, 'filtered_fastq_output.xlsx', 'xlsx')\r\n\r\n## Contributing\r\n\r\nContributions to Bio-Wrangler are welcome! If you have any bug reports, feature requests, or pull requests, please follow the guidelines in the **CONTRIBUTING.md** file.\r\n\r\n## License\r\n\r\nThis project is licensed under the MIT License. See the [LICENSE](LICENSE) file for details.\r\n\r\n---\r\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fse7en69%2Fbio-wrangler","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fse7en69%2Fbio-wrangler","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fse7en69%2Fbio-wrangler/lists"}