import sys
import init
with file('../../data/ref.cmap') as f:
ref = init.read_ref(f)
with file('../../data/input.bnx') as f:
moles = init.read_moles(f)
mole_id = int(sys.argv[1])
print 'mole:'
print moles[mole_id]
start_site = int(sys.argv[2])
end_site = int(sys.argv[3])
result = []
print 'ref:'
for i in xrange(end_site - start_site + 1):
result.append(ref[start_site + i])
print result
'''
for i in xrange(rows):
for j in xrange(cols):
print '%f '%score_matrix[i][j],
print
#print the score_matrix
for i in xrange(rows + 1):
for j in xrange(cols + 1):
print "%f "%score_matrix[i][j],
print
'''
#get the trace of DP
#TODO
if __name__ == '__main__':
if len(sys.argv) < 3:
print 'INPUT ERROR: Two files is needs. The first file is mole file(*.inx), and another is reference file(*.cmp)'
exit()
with file(sys.argv[1]) as f:
moleset = init.read_moles(f)
with file(sys.argv[2]) as f:
ref = init.read_ref(f)[1 : ]
#print 'ref: '
#print ref
for mole in moleset:
print 'mole: %d'%mole
#print moleset[mole]
DP(moleset[mole], ref)
