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#!/usr/bin/env python
# Copyright 2000-2001 by Brad Chapman. All rights reserved.
# Revisions copyright 2007-2003 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""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
from __future__ import print_function
import os
# biopython
from Bio import Alphabet
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC
from Bio.Align import AlignInfo
from Bio import AlignIO
from Bio.SubsMat import FreqTable
from Bio.Align import MultipleSeqAlignment
# Very simple tests on an empty alignment
alignment = MultipleSeqAlignment([], Alphabet.generic_alphabet)
assert alignment.get_alignment_length() == 0
assert len(alignment) == 0
del alignment
# Basic tests on simple three string alignment
alignment = MultipleSeqAlignment([], Alphabet.generic_alphabet)
letters = "AbcDefGhiJklMnoPqrStuVwxYz"
alignment.append(SeqRecord(Seq(letters), id="mixed"))
alignment.append(SeqRecord(Seq(letters.lower()), id="lower"))
alignment.append(SeqRecord(Seq(letters.upper()), id="upper"))
assert alignment.get_alignment_length() == 26
assert len(alignment) == 3
assert str(alignment[0].seq) == letters
assert str(alignment[1].seq) == letters.lower()
assert str(alignment[2].seq) == letters.upper()
assert alignment[0].id == "mixed"
assert alignment[1].id == "lower"
assert alignment[2].id == "upper"
for (col, letter) in enumerate(letters):
assert alignment[:, 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], MultipleSeqAlignment)
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 = AlignIO.read(test_file, "clustal")
# print the alignment back out
print(alignment.format("clustal"))
alignment = AlignIO.read(os.path.join(test_dir, test_names[0]), "clustal",
alphabet=Alphabet.Gapped(IUPAC.unambiguous_dna))
# test the base alignment stuff
print('all_seqs...')
for seq_record in alignment:
print('description: %s' % seq_record.description)
print('seq: %r' % seq_record.seq)
print('length: %i' % alignment.get_alignment_length())
print('Calculating summary information...')
align_info = AlignInfo.SummaryInfo(alignment)
consensus = align_info.dumb_consensus()
assert isinstance(consensus, Seq)
print('consensus: %r' % consensus)
print('Replacement dictionary')
ks = sorted(align_info.replacement_dictionary(['N']))
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[1].seq
print(align_info.pos_specific_score_matrix(second_seq, ['N']))
print('information content')
print('part of alignment: %0.2f'
% align_info.information_content(5, 50, chars_to_ignore=['N']))
print('entire alignment: %0.2f'
% 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: %0.2f'
% align_info.information_content(e_freq_table=e_freq_table,
chars_to_ignore=['N']))
print('Column 1: %s' % align_info.get_column(1))
print('IC for column 1: %0.2f' % align_info.ic_vector[1])
print('Column 7: %s' % align_info.get_column(7))
print('IC for column 7: %0.2f' % 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(to_parse, "fasta",
alphabet=Alphabet.Gapped(IUPAC.ambiguous_dna))
# test the base alignment stuff
print('all_seqs...')
for seq_record in alignment:
print('description: %s' % seq_record.description)
print('seq: %r' % seq_record.seq)
print('length: %i' % alignment.get_alignment_length())
align_info = AlignInfo.SummaryInfo(alignment)
consensus = align_info.dumb_consensus(ambiguous="N", threshold=0.6)
assert isinstance(consensus, Seq)
print('consensus: %r' % consensus)
print(alignment)
print("Test format conversion...")
# parse the alignment file and get an aligment object
alignment = AlignIO.read(os.path.join(os.curdir, 'Clustalw', 'opuntia.aln'),
'clustal')
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("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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