skills/bioskills/bio-comparative-genomics-hgt-detection/scripts/hgt_detection.py

• calculate_gc_content · function · L9-L14 — def calculate_gc_content(sequence)
• genome_gc_stats · function · L17-L29 — def genome_gc_stats(cds_sequences)
• identify_gc_anomalies · function · L32-L57 — def identify_gc_anomalies(cds_sequences, z_threshold=2)
• calculate_codon_usage · function · L60-L71 — def calculate_codon_usage(cds_sequence)
• genome_codon_usage · function · L74-L86 — def genome_codon_usage(cds_sequences)
• codon_usage_deviation · function · L89-L104 — def codon_usage_deviation(gene_codon_usage, genome_codon_usage)
• identify_codon_anomalies · function · L107-L124 — def identify_codon_anomalies(cds_sequences, percentile_threshold=95)
• identify_genomic_islands · function · L127-L164 — def identify_genomic_islands(gene_annotations, max_gap=10000, min_genes=3)
• summarize_hgt_analysis · function · L167-L192 — def summarize_hgt_analysis(gc_anomalies, gc_stats, codon_anomalies, islands)