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test_align.py

#!/usr/bin/env python
"""test_align.py

A script to test alignment stuff.

Right now we've got tests for:
o Reading and Writing clustal format
o Reading and Writing fasta format
o Converting between formats"""

# standard library
import os 

# biopython
from Bio import Alphabet
from Bio import Seq
from Bio.Alphabet import IUPAC
from Bio import Clustalw
from Bio.Align import AlignInfo
from Bio import AlignIO
from Bio.SubsMat import FreqTable
from Bio.Align.Generic import Alignment

#Very simple tests on an empty alignment
alignment = Alignment(Alphabet.generic_alphabet)
assert alignment.get_alignment_length() == 0
assert len(alignment) == 0
del alignment

#Basic tests on simple three string alignment
alignment = Alignment(Alphabet.generic_alphabet)
letters = "AbcDefGhiJklMnoPqrStuVwxYz"
alignment.add_sequence("mixed", letters)
alignment.add_sequence("lower", letters.lower())
alignment.add_sequence("upper", letters.upper())
assert alignment.get_alignment_length() == 26
assert len(alignment) == 3
assert alignment.get_seq_by_num(0).tostring() == letters
assert alignment.get_seq_by_num(1).tostring() == letters.lower()
assert alignment.get_seq_by_num(2).tostring() == letters.upper()
assert alignment[0].description == "mixed"
assert alignment[1].description == "lower"
assert alignment[2].description == "upper"
for (col, letter) in enumerate(letters):
    assert alignment.get_column(col) == letter \
                                      + letter.lower() \
                                      + letter.upper()
#Check row extractions:
assert alignment[0].id == "mixed"
assert alignment[-1].id == "upper"
#Check sub-alignment extraction by row slicing:
assert isinstance(alignment[::-1], Alignment)
assert alignment[::-1][0].id == "upper"
assert alignment[::-1][2].id == "mixed"

del alignment
del letters

print "testing reading and writing clustal format..."
test_dir = os.path.join(os.getcwd(), 'Clustalw')
test_names = ['opuntia.aln', 'cw02.aln']

test_files = []
for name in test_names:
    test_files.append(os.path.join(test_dir, name))

for test_file in test_files:
    # parse the alignment file and get an aligment object
    alignment = Clustalw.parse_file(test_file)

    # print the alignment back out
    print alignment

alignment = Clustalw.parse_file(os.path.join(test_dir, test_names[0]))

# test the base alignment stuff
print 'all_seqs...'
for seq_record in alignment:
    print 'description:', seq_record.description
    print 'seq:', repr(seq_record.seq)
print 'length:', alignment.get_alignment_length()

print 'Calculating summary information...'
align_info = AlignInfo.SummaryInfo(alignment)
consensus = align_info.dumb_consensus()
assert isinstance(consensus, Seq.Seq)
print 'consensus:', repr(consensus)


print 'Replacement dictionary'
ks = align_info.replacement_dictionary(['N']).keys()
ks.sort()
for key in ks:
    print "%s : %s" % (key, align_info.replacement_dictionary(['N'])[key])

print 'position specific score matrix.'
print 'with a supplied consensus sequence...'
print align_info.pos_specific_score_matrix(consensus, ['N'])

print 'defaulting to a consensus sequence...'
print align_info.pos_specific_score_matrix(chars_to_ignore = ['N'])

print 'with a selected sequence...'
second_seq = alignment.get_seq_by_num(1)
print align_info.pos_specific_score_matrix(second_seq, ['N'])

print 'information content'
print 'part of alignment:', align_info.information_content(5, 50,
                                chars_to_ignore = ['N'])
print 'entire alignment:', align_info.information_content(
                                chars_to_ignore = ['N'])

print 'relative information content'
e_freq = {'G' : 0.25,
          'C' : 0.25,
          'A' : 0.25,
          'T' : 0.25}

e_freq_table = FreqTable.FreqTable(e_freq, FreqTable.FREQ,
                                   IUPAC.unambiguous_dna)

print 'relative information:', align_info.information_content(
                                   e_freq_table = e_freq_table,
                                   chars_to_ignore = ['N'])

print 'Column 1:', align_info.get_column(1)
print 'IC for column 1:', align_info.ic_vector[1]
print 'Column 7:', align_info.get_column(7)
print 'IC for column 7:', align_info.ic_vector[7]
print 'test print_info_content'
AlignInfo.print_info_content(align_info)
print "testing reading and writing fasta format..."

to_parse = os.path.join(os.curdir, 'Quality', 'example.fasta')

alignment = AlignIO.read(open(to_parse), "fasta",
                         alphabet = Alphabet.Gapped(IUPAC.ambiguous_dna))

# test the base alignment stuff
print 'all_seqs...'
for seq_record in alignment:
    print 'description:', seq_record.description
    print 'seq:', repr(seq_record.seq)

print 'length:', alignment.get_alignment_length()
align_info = AlignInfo.SummaryInfo(alignment)
consensus = align_info.dumb_consensus(ambiguous="N", threshold=0.6)
assert isinstance(consensus, Seq.Seq)
print 'consensus:', repr(consensus)

print alignment


print "Test format conversion..."

# parse the alignment file and get an aligment object
alignment = Clustalw.parse_file(os.path.join(os.curdir, 'Clustalw',
                                             'opuntia.aln'))

print "As FASTA:"
print alignment.format("fasta")
print "As Clustal:"
print alignment.format("clustal")

"""
# test to find a position in an original sequence given a
# column position in an alignment
print "Testing finding column positions..."
alignment_info = ["GATC--CGATC--G",
                  "GA--CCCG-TC--G",
                  "GAT--CC--TC--G"]

gapped_unambiguous = Alphabet.Gapped(IUPAC.unambiguous_dna)

alignment = Alignment(gapped_unambiguous)
for seq in alignment_info:
    alignment.add_sequence("Blah", seq)

test_seq_1 = Seq.Seq("GATCCGATCG")
orig_pos = alignment.original_sequence_pos(3, test_seq_1, 0)
assert orig_pos == 3, "Got unexpected position: %s" % orig_pos
orig_pos = alignment.original_sequence_pos(7, test_seq_1, 0)
assert orig_pos == 5, "Got unexpected position: %s" % orig_pos
orig_pos = alignment.original_sequence_pos(0, test_seq_1, 0)
assert orig_pos == 0, "Got unexpected position: %s" % orig_pos
orig_pos = alignment.original_sequence_pos(13, test_seq_1, 0)
assert orig_pos == 9, "Got unexpected position: %s" % orig_pos

try:
    orig_pos = alignment.original_sequence_pos(5, test_seq_1, 0)
    raise AssertionError("Did not fail with a junk position")
except AssertionError:
    pass
"""

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