#!/usr/bin/env python
"""clustal_run.py
 
Example code to show how to create a clustalw command line, run clustalw
and parse the results into an object that can be dealt with easily."""
# standard library
 
from __future__ import print_function
 
import os
import sys
import subprocess
 
# biopython
from Bio.Alphabet import Gapped, IUPAC
from Bio.Align.Applications import ClustalwCommandline
from Bio import AlignIO
from Bio.Align import AlignInfo
from Bio.SubsMat import FreqTable
 
# create the command line to run clustalw
# this assumes you've got clustalw somewhere on your path, otherwise
# you need to pass the full path of the executable to this via cmd="..."
cline = ClustalwCommandline(infile='opuntia.fasta', outfile='test.aln')
 
# actually perform the alignment
return_code = subprocess.call(str(cline), shell=(sys.platform != "win32"))
assert return_code == 0, "Calling ClustalW failed"
 
# Parse the output
alignment = AlignIO.read("test.aln", "clustal",
                         alphabet=Gapped(IUPAC.unambiguous_dna))
 
print(alignment)
 
print('first description: %s' % alignment[0].description)
print('first sequence: %s' % alignment[0].seq)
 
# get the length of the alignment
print('length %i' % alignment.get_alignment_length())
 
print(alignment)
 
# print out interesting information about the alignment
summary_align = AlignInfo.SummaryInfo(alignment)
 
consensus = summary_align.dumb_consensus()
print('consensus %s' % consensus)
 
my_pssm = summary_align.pos_specific_score_matrix(consensus,
                                                  chars_to_ignore=['N'])
 
print(my_pssm)
 
expect_freq = {
    'A': .3,
    'G': .2,
    'T': .3,
    'C': .2}
 
freq_table_info = FreqTable.FreqTable(expect_freq, FreqTable.FREQ,
                                      IUPAC.unambiguous_dna)
 
info_content = summary_align.information_content(5, 30,
                                                 chars_to_ignore=['N'],
                                                 e_freq_table=freq_table_info)
 
print("relative info content: %f" % info_content)