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))
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))