def analyze_insertions(fa, threads = <NUM_LIT:6>):
safe, sequences, id2name, names, insertions = analyze_fa(fa)<EOL>seqs = seq_info(names, id2name, insertions, sequences)<EOL>seqs, orfs = find_orfs(safe, seqs)<EOL>seqs = find_introns(safe, seqs, sequences, threads)<EOL>seqs = seqs2bool(seqs)<EOL>seqs = annotate_orfs(orfs, seqs, threads)<EOL>return seqs, id2name<EOL>
- find ORFs using Prodigal
- find introns using cmscan (vs Rfam intron database)
- check that ORFs and intron overlap with insertion region
- plot insertion length versus model position for each insertion (based on insertion type)