def summary(args): """ %prog summary old.new.chain old.fasta new.fasta Provide stats of the chain file. """ from jcvi.formats.fasta import summary as fsummary from jcvi.utils.cbook import percentage, human_size p = OptionParser(summary.__doc__) opts, args = p.parse_args(args) if len(args) != 3: sys.exit(not p.print_help()) chainfile, oldfasta, newfasta = args chain = Chain(chainfile) ungapped, dt, dq = chain.ungapped, chain.dt, chain.dq print >> sys.stderr, "File `{0}` contains {1} chains.".\ format(chainfile, len(chain)) print >> sys.stderr, "ungapped={0} dt={1} dq={2}".\ format(human_size(ungapped), human_size(dt), human_size(dq)) oldreal, oldnn, oldlen = fsummary([oldfasta, "--outfile=/dev/null"]) print >> sys.stderr, "Old fasta (`{0}`) mapped: {1}".\ format(oldfasta, percentage(ungapped, oldreal)) newreal, newnn, newlen = fsummary([newfasta, "--outfile=/dev/null"]) print >> sys.stderr, "New fasta (`{0}`) mapped: {1}".\ format(newfasta, percentage(ungapped, newreal))