def main():
# Parse command line arguments
options, args = doc_optparse.parse( __doc__ )
try:
lnorm = bool( options.lnorm )
recalculate = bool( options.recalculate )
except:
doc_optparse.exit()
hox70 = score.build_scoring_scheme( """ A C G T
91 -114 -31 -123
-114 100 -125 -31
-31 -125 100 -114
-123 -31 -114 91 """, 400, 30, default=0 )
maf_reader = maf.Reader( sys.stdin )
for m in maf_reader:
if m.text_size == 0:
print "NA"
continue
s = m.score
# Recalculate?
if recalculate:
s = hox70.score_alignment( m )
# Normalize?
if lnorm:
s = s / m.text_size
# Print
print s
def main():
# Parse command line arguments
options, args = doc_optparse.parse(__doc__)
try:
lnorm = bool(options.lnorm)
recalculate = bool(options.recalculate)
except Exception:
doc_optparse.exit()
hox70 = score.build_scoring_scheme(""" A C G T
91 -114 -31 -123
-114 100 -125 -31
-31 -125 100 -114
-123 -31 -114 91 """,
400,
30,
default=0)
maf_reader = maf.Reader(sys.stdin)
for m in maf_reader:
if m.text_size == 0:
print("NA")
continue
s = m.score
# Recalculate?
if recalculate:
s = hox70.score_alignment(m)
# Normalize?
if lnorm:
s = s / m.text_size
# Print
print(s)