def test_alignment(self):
self.assertEqual(len(self.sum_rec), self.head_rec.nalign)
alignment = FSSPTools.mult_align(self.sum_rec, self.align_rec)
name_list = ["2hvm0", "1hvq0", "1nar0", "2ebn0"]
sum_newnames, align_newnames = FSSPTools.name_filter(
self.sum_rec, self.align_rec, name_list)
self.assertEqual(len(sum_newnames), 4)
line = """\
2: 1cnv 2hvm 39.2 1.7 270 273 42 0 0 10 S hevamine (chitinaseLYSOZYME)
""" # noqa : W291
self.assertEqual(str(sum_newnames[2]), line)
line = """\
3: 1cnv 1hvq 39.0 1.7 271 273 41 0 0 10 S hevamine a
""" # noqa : W291
self.assertEqual(str(sum_newnames[3]), line)
line = """\
5: 1cnv 1nar 20.0 3.1 246 289 13 0 0 27 S Narbonin
""" # noqa : W291
self.assertEqual(str(sum_newnames[5]), line)
line = """\
11: 1cnv 2ebn 16.9 3.0 215 285 13 0 0 25 S Endo-beta-n-acetylglucosaminidase f1 (endoglycosidase f
""" # noqa : W291
self.assertEqual(str(sum_newnames[11]), line)
new_dict = align_newnames["0P168"].pos_align_dict
self.assertEqual(len(new_dict), 4)
self.assertEqual(str(new_dict[2]), "Ps")
self.assertEqual(str(new_dict[3]), "Ps")
self.assertEqual(str(new_dict[5]), "..")
self.assertEqual(str(new_dict[11]), "..")
f = sys.stdout
f.write("\nRead in %s\n" % os.path.basename(test_file))
handle = open(test_file)
head_rec, sum_rec, align_rec = FSSP.read_fssp(handle)
handle.close()
f.write("...1cnv.fssp read\n")
for i in [
"author", "compnd", "database", "header", "nalign", "pdbid",
"seqlength", "source"
]:
f.write('head_rec.%s %s\n' % (i, str(getattr(head_rec, i))))
f.write("\nlen(sum_rec) = %d; head_rec.nalign = %d\n" %
(len(sum_rec), head_rec.nalign))
f.write("The above two numbers should be the same\n")
f.write("\nCreate a multiple alignment instance using Bio.Align\n")
alignment = FSSPTools.mult_align(sum_rec, align_rec)
f.write("...Done\n")
# Percent ID filtering takes too long.. remove from test.
# f.write("\nFilter in percent ID's >= 15%\n")
# sum_ge_15, align_ge_15 = FSSPTools.filter(sum_rec, align_rec, 'pID', 15,100)
# f.write("\nnumber of records filtered in: %d\n" % len(sum_ge_15))
# k = sorted(sum_ge_15)
# f.write("\nRecords filtered in %s\n" % k)
# Pickling takes too long.. remove from test.
# f.write("\nLet's Pickle this\n")
# dump_file = os.path.join('FSSP', 'mydump.pik')
# pickle.dump((head_rec, sum_rec, align_rec),open(dump_file, 'w'))
f.write("\nFilter by name\n")
test_file = os.path.join('FSSP', '1cnv.fssp')
f = sys.stdout
f.write("\nRead in %s\n" % os.path.basename(test_file))
handle = open(test_file)
head_rec, sum_rec, align_rec = FSSP.read_fssp(handle)
handle.close()
f.write("...1cnv.fssp read\n")
for i in ["author", "compnd", "database", "header", "nalign",
"pdbid", "seqlength", "source"]:
f.write('head_rec.%s %s\n' % (i, str(getattr(head_rec,i))))
f.write("\nlen(sum_rec) = %d; head_rec.nalign = %d\n" %
(len(sum_rec), head_rec.nalign))
f.write("The above two numbers should be the same\n")
f.write("\nCreate a multiple alignment instance using Bio.Align\n")
alignment = FSSPTools.mult_align(sum_rec, align_rec)
f.write("...Done\n")
# Percent ID filtering takes too long.. remove from test.
# f.write("\nFilter in percent ID's >= 15%\n")
# sum_ge_15, align_ge_15 = FSSPTools.filter(sum_rec, align_rec, 'pID', 15,100)
# f.write("\nnumber of records filtered in: %d\n" % len(sum_ge_15))
# k = sum_ge_15.keys()
# k.sort()
# f.write("\nRecords filtered in %s\n" % k)
# Pickling takes too long.. remove from test.
# f.write("\nLet's Pickle this\n")
# dump_file = os.path.join('FSSP', 'mydump.pik')
# cPickle.dump((head_rec, sum_rec, align_rec),open(dump_file, 'w'))