alignment.to_profile() -- convert alignment to profile format

clean_sequences = <bool:1>

True

whether or not clean non-standard residues

Description:

This command will convert the alignment, currently in memory, into the profile format. For more details on the profile format, see profile.read().

If clean_sequences is set to 'on', then the non-standard residues in the sequences will be cleaned before transferring into the profile format. Specifically, ASX (B) will be replaced with ASN (N), GLX (Z) will be replaced with GLN (Q) and UNK (X) will be replaced with ALA (A).

Example: examples/commands/aln_to_prof.py

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(clean_sequences=True)

# 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')