from modeller import *
env = Environ()

# Read in the alignment file
aln = Alignment(env)
aln.append(file='toxin.ali', alignment_format='PIR', align_codes='ALL')

# Convert the alignment to profile format
prf = aln.to_profile()

# Write out the profile

# in text file
prf.write(file='alntoprof.prf', profile_format='TEXT')

# in binary format
prf.write(file='alntoprof.bin', profile_format='BINARY')