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clustal_run.py
#!/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
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:', alignment[0].description
print 'first sequence:', alignment[0].seq

# get the length of the alignment
print 'length', 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', 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:", info_content


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