Profile.to_alignment() — profile to alignment

to_alignment()

Output:

alignment

This command will convert a profile that is in memory into the alignment format (see Section B.1). The function of this command is complimentary to Alignment.to_profile(). The generated alignment is returned.

Note: Not all information of a 'PIR' format is encoded in a profile. (See Profile.read()). So converting a profile to an alignment may need manual attention to ensure that the alignment is useful for other routines.

Example: examples/commands/read_profile.py

# Example file for: Profile.read(), Profile.to_alignment()

from modeller import *

env = Environ()

# Create a new, blank, profile
prf = Profile(env)

# Read in the profile file
prf.read(file='toxin.prf', profile_format='TEXT')

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

# Write out the alignment
aln.write(file='readprofile.pir', alignment_format='PIR')