注释基因组文件 contig.gff 或者 scaffold.gff to chromosome gff
python3 -m jcvi.formats.chain fromagp genome.final.agp contig.fa genome.fa
得到：genome.final.chain 再用 liftover转换：http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver
liftOver -gff contig.gff3 genome.final.chain genome.gff3 unmapped
The arguments are:
- contig.gff3: scaffold annotations (INPUT)
- contig_to_genome.chain: translations (INPUT)
- genome.gff3: genome annotations (OUTPUT)
- unmapped: things that fail (OUTPUT)
或者用
CrossMap.py gff genome.final.chain contig.gff genome.gff
