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# Copyright 2008 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.
import os
from StringIO import StringIO
from Bio import AlignIO
from Bio import Clustalw
from Bio.Align.Generic import Alignment
# test_files is a list of tuples containing:
# - integer: number of sequences per alignment
# - integer: number of alignments
# - string: relative filename
test_files = [ \
#clustalw 1.81
(2, 1, 'Clustalw/cw02.aln'),
(7, 1, 'Clustalw/opuntia.aln'),
(20, 1, 'Clustalw/protein.aln'),
# clustalw 2.0.8
(2, 1, 'Clustalw/odd_consensus.aln'),
# clustalw 2.0.9
(5, 1, 'Clustalw/hedgehog.aln'),
# PROMALS3D
(20, 1, 'Clustalw/promals3d.aln'),
]
def compare(a1, a2):
assert a1.get_alignment_length() == a2.get_alignment_length()
assert len(a1._records) == len(a2._records)
for r1, r2 in zip(a1,a2):
assert r1.id == r2.id
assert str(r1.seq) == str(r2.seq)
if hasattr(a1, "_version") and a1._version \
and hasattr(a2, "_version") and a2._version:
assert a1._version == a2._version
if hasattr(a1, "_star_info") and a1._star_info \
and hasattr(a2, "_star_info") and a2._star_info:
assert a1._star_info == a2._star_info \
return True
print "Checking Bio.AlignIO and Bio.Clustalw can read example files..."
for (t_per, t_count, t_filename) in test_files:
print
print "Testing reading %s format file %s with %i alignments" \
% ("clustal", t_filename, t_count)
assert os.path.isfile(t_filename), t_filename
print "Using Bio.AlignIO.parse(...)"
alignments = list(AlignIO.parse(handle=open(t_filename,"r"), format="clustal"))
assert len(alignments) == t_count, \
"Found %i alignments but expected %i" % (len(alignments), t_count)
for alignment in alignments:
assert len(alignment) == t_per, \
"Expected %i records per alignment, got %i" \
% (t_per, len(alignment))
print
print alignment
if t_count != 1 : continue
print
# Check Bio.AlignIO.read(...)
alignment = AlignIO.read(handle=open(t_filename), format="clustal")
assert isinstance(alignment, Alignment)
assert compare(alignment, alignments[0])
print "Using Bio.AlignIO.read(...)"
#print "~" * 75
#handle = StringIO()
#AlignIO.write([alignment], handle, "clustal")
#handle.seek(0)
#print handle.read()
#print "~" * 75
print "Using Bio.Clustalw.parse_file(...)"
c_alignment = Clustalw.parse_file(t_filename)
assert isinstance(c_alignment, Alignment)
assert isinstance(c_alignment, Clustalw.ClustalAlignment)
#print " Using Bio.Clustalw.parse_file(...)"
#print "~" * 75
#print c_alignment
#print "~" * 75
#print
# Compare the two...
assert compare(alignment, c_alignment)
# Check Bio.AlignIO can read the Bio.Clustalw's string output
n_alignment = AlignIO.read(StringIO(str(c_alignment)), "clustal")
assert isinstance(alignment, Alignment)
assert compare(n_alignment, c_alignment)
print "Finished tested reading files"
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