# profile-profile alignment using salign
from modeller import *

log.level(1, 0, 1, 1, 1)
env = environ()

aln = alignment(env, file='mega_prune.faa', alignment_format='FASTA')

aln.salign(rr_file='${LIB}/blosum62.sim.mat',
           gap_penalties_1d=(-500, 0), output='',
           align_block=15,   # no. of seqs. in first MSA
           align_what='PROFILE',
           alignment_type='PAIRWISE',
           comparison_type='PSSM',  # or 'MAT' (Caution: Method NOT benchmarked
                                    # for 'MAT')
           similarity_flag=True,    # The score matrix is not rescaled
           substitution=True,       # The BLOSUM62 substitution values are
                                    # multiplied to the corr. coef.
           #write_weights=True,
           #output_weights_file='test.mtx', # optional, to write weight matrix
           smooth_prof_weight=10.0) # For mixing data with priors

#write out aligned profiles (MSA)
aln.write(file='salign.ali', alignment_format='PIR')

# Make a pairwise alignment of two sequences
aln = alignment(env, file='salign.ali', alignment_format='PIR',
                align_codes=('12asA', '1b8aA'))
aln.write(file='salign_pair.ali', alignment_format='PIR')
aln.write(file='salign_pair.pap', alignment_format='PAP')