skills/bioskills/bio-comparative-genomics-synteny-analysis/scripts/synteny_analysis.py

• prepare_gff_for_mcscanx · function · L9-L46 — def prepare_gff_for_mcscanx(gff_file, output_file, species_prefix)
• run_blastp · function · L49-L67 — def run_blastp(fasta1, fasta2, output_file, evalue=1e-10, num_threads=4)
• run_mcscanx · function · L70-L87 — def run_mcscanx(prefix, min_genes=5, max_gaps=25)
• parse_collinearity_file · function · L90-L125 — def parse_collinearity_file(collinearity_file)
• summarize_synteny · function · L128-L161 — def summarize_synteny(blocks)
• detect_wgd_signature · function · L164-L189 — def detect_wgd_signature(blocks, ks_values=None)