axp-knickei/CirculAn: CirculAn v0.1.0: Initial Release of Genomic Visualization & Annotation Toolkit

We are excited to announce the first release of CirculAn, a Python script to streamline the transition from raw genomic data to publication-quality visualizations. This release can be used for bacterial genome characterization, focusing on structural features and functional distribution. Key Features Circular Genome Mapping (circular_genome_map_publication.py) Visualization: Generates 600 DPI circular maps. Structural Tracks: Automated plotting of Forward/Reverse CDS tracks, GC Content, and GC Skew. GC Calculation: Implements sliding-window algorithms for GC metrics with customizable window and step sizes. Visual Fills: Includes area fills for GC Content (baseline-anchored) and GC Skew (green/purple directional fills). Styling: Features refined typography, vector graphics export (SVG), and clear genomic position markers. Functional Profile Visualization (plot_nature_figure.py & generate_scientific_figure.py) Donut Charts: A modern visualization tool for EggNOG-mapper and COG results, featuring central data summaries and optimized slice ordering. Scientific Color Palettes: Logic-based coloring (e.g., metabolism in greens, information processing in blues) using colorblind-friendly schemes. Flexible Input Handling: Support for direct CSV summaries or automated parsing of Galaxy-exported tabular files. Data Processing Utilities create_fasta.py: An utility to extract and validate protein sequences from XLSX annotation files, ensuring compatibility with downstream orthology tools. create_functional_table.py: An automated parser for EggNOG-mapper .annotations files that handles concatenated category codes and computes statistical distributions. 🛠 Technical Specifications * Environment Management: Full support for uv for lightning-fast, reproducible dependency resolution. * Dependencies: Optimized for pandas, matplotlib, numpy, and seaborn. * Outputs: All tools generate dual-format outputs—PNG for immediate review and SVG/PDF for lossless manuscript integration.