def setup():
"""Create fixtures"""
# Define chromosome sizes
Read.extract_chromosome_sizes([
"@HD\tVN:1.0\tSO:unsorted", "@SQ\tSN:chr1\tLN:300",
"@SQ\tSN:chr2\tLN:200", "@PG\tID:test\tVN:0.1"
])
Feature.process_set_chromosome_conversion(["1\tchr1", "2\tchr2"])
good_input["bed input counting all of the read"] = (
"all",
"[17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]"
)
good_input["bed input counting start of the read"] = (
"start", "[17, 18, 19, 20, 21, 22, 23]")
good_input["bed input counting end of the read"] = (
"end", "[36, 37, 38, 39, 40, 41, 42]")
good_input["gff input counting all of the read"] = (
"all",
"[43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8]"
)
good_input["gff input counting start of the read"] = (
"start", "[43, 42, 41, 40, 39, 38, 37]")
good_input["gff input counting end of the read"] = (
"end", "[14, 13, 12, 11, 10, 9, 8]")
for method in ['all', 'start', 'end']:
print "\nTesting feature_count option: ****{}****".format(method)
if method == 'all':
metagene = Metagene(10, 4, 2)
print "\t with Metagene:\t{}".format(metagene)
print "\t with chromosome conversions:\t{}".format(
Feature.chromosome_conversion)
else:
metagene = Metagene(1, 4, 2)
print "\t with Metagene:\t{}".format(metagene)
print "\t with chromosome conversions:\t{}".format(
Feature.chromosome_conversion)
# create feature from BED line
try:
bedline = "{}\t{}\t{}\t{}\t{}\t{}\n".format(
1, 20, 40, "first", 44, "+")
print "\t with BED line:\t{}".format(bedline.strip())
feature1 = Feature.create_from_bed(method, metagene, bedline,
False, False)
if str(feature1.position_array) != correct_features['bed'][method]:
print "**FAILED**\t Create Feature from BED line ?"
print "\t Desired positions:\t{}".format(
correct_features['bed'][method])
print "\t Created positions:\t{}".format(
feature1.position_array)
except MetageneError as err:
print "**FAILED**\t Create Feature from BED line ?"
else:
print "PASSED\t Create Feature from BED line ?\t\t{}".format(
feature1.get_chromosome_region())
# create feature from GFF line
try:
gffline = "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(
2, "test", "gene", 10, 39, ".", "-", ".", "second")
print "\t with GFF line:\t{}".format(gffline.strip())
feature2 = Feature.create_from_gff(method, metagene, gffline,
False, False)
if str(feature2.position_array) != correct_features['gff'][method]:
print "**FAILED**\t Create Feature from GFF line ?\t**FAIL**"
print "\t Desired positions:\t{}".format(
correct_features['gff'][method])
print "\t Created positions:\t{}".format(
feature2.position_array)
except MetageneError as err:
print "**FAILED**\t Create Feature from GFF line ?"
else:
print "PASSED\t Create Feature from GFF line ?\t\t{}".format(
feature2.get_chromosome_region())
# create feature from GFF line with start and end swapped
try:
gffline = "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(
2, "test", "gene", 39, 10, ".", "-", ".", "second")
print "\t with GFF line:\t{}".format(gffline.strip())
feature2 = Feature.create_from_gff(method, metagene, gffline,
False, False)
if str(feature2.position_array) != correct_features['gff'][method]:
print "**FAILED**\t Create Feature from GFF line with swapped start and end ?\t**FAIL**"
print "\t Desired positions:\t{}".format(
correct_features['gff'][method])
print "\t Created positions:\t{}".format(
feature2.position_array)
except MetageneError as err:
print "**FAILED**\t Create Feature from GFF line with swapped start and end ?"
else:
print "PASSED\t Create Feature from GFF line with swapped start and end ?\t\t{}".format(
feature2.get_chromosome_region())
try:
gffline = "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(
2, "test", "gene", 39, 10, ".", "+", ".", "second")
print "\t with GFF line:\t{}".format(gffline.strip())
feature2 = Feature.create_from_gff(method, metagene, gffline,
False, False)
if str(feature2.position_array) != correct_features['gff'][method]:
print "**FAILED**\t Do not create Feature from GFF line with swapped start and end, + strand ?\t**FAIL**"
print "\t Desired positions:\t{}".format(
correct_features['gff'][method])
print "\t Created positions:\t{}".format(
feature2.position_array)
except MetageneError as err:
print "PASSED\t Do not create Feature from GFF line with swapped start and end, + strand ?\t\t{}".format(
err)
else:
print "**FAILED**\t Do not create Feature from GFF line with swapped start and end, + strand ?\t\t{}".format(
feature2.get_chromosome_region())
##TODO finish complete testing of Feature class
print "\n##TODO finish testing of Feature class creation\n"
print "\n**** Testing counting and maniputlation ****\n"
expected = {'all': {}, 'start': {}, 'end': {}}
# Positions in metagene: 17 18 19 20 21-22,23-24,25-26,27-28,29-30,31-32,33-34,35-36,37-38,39-40, 41, 42
expected['all'] = {
'all':
"first,sense:allreads,0.333,0.333,0.000,0.000,0.000,0.000,0.000,0.000,0.286,0.571,0.571,0.000,0.000,0.286,0.286,0.000\nfirst,antisense:allreads,0.000,0.000,0.000,0.000,0.000,0.100,0.100,0.100,0.100,0.100,0.000,0.000,0.000,0.000,0.000,0.111",
'start':
"first,sense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,2.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000\nfirst,antisense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.500,0.000,0.000,0.000,0.000,0.000,0.000",
'end':
"first,sense:allreads,0.000,3.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,2.000,0.000\nfirst,antisense:allreads,0.000,0.000,0.000,0.000,0.000,0.500,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,1.000"
}
# Positions in metagene: 17 18 19 20 [21] 22 23
expected['start'] = {
'all':
"first,sense:allreads,0.333,0.333,0.000,0.000,0.000,0.000,0.000\nfirst,antisense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,0.050",
'start':
"first,sense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,0.000\nfirst,antisense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,0.000",
'end':
"first,sense:allreads,0.000,3.000,0.000,0.000,0.000,0.000,0.000\nfirst,antisense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,0.500"
}
# Positions in metagene: 36 37 38 39 [40] 41 42
expected['end'] = {
'all':
"first,sense:allreads,0.000,0.000,0.000,0.000,0.286,0.286,0.000\nfirst,antisense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,0.111",
'start':
"first,sense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,0.000\nfirst,antisense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,0.000",
'end':
"first,sense:allreads,0.000,0.000,0.000,0.000,0.000,2.000,0.000\nfirst,antisense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,1.000"
}
metagene = {
'all': Metagene(10, 4, 2),
'start': Metagene(1, 4, 2),
'end': Metagene(1, 4, 2)
}
for method in ['all', 'start', 'end']:
if method == 'all':
print "\t with Metagene:\t{}".format(metagene[method])
print "\t with chromosome conversions:\t{}".format(
Feature.chromosome_conversion)
else:
print "\t with Metagene:\t{}".format(metagene[method])
print "\t with chromosome conversions:\t{}".format(
Feature.chromosome_conversion)
print "\nTesting feature_count option: ****{}****".format(method)
feature_line = "{}\t{}\t{}\t{}\t{}\t{}\n".format(
1, 20, 40, "first", 44, "+")
feature1 = Feature.create_from_bed(method, metagene[method],
feature_line, False, False)
print "\tFeature:\t{}".format(feature1.position_array)
reads = []
reads.append(
Read("chr1", "+", 3, 1, [10, 11, 12, 13, 14, 15, 16, 17, 18]))
reads.append(
Read("chr1", "-", 1, 2, [23, 24, 25, 26, 27, 28, 29, 30, 31, 32]))
reads.append(Read("chr1", "+", 4, 2, [30, 31, 32, 33, 34, 40, 41]))
reads.append(
Read("chr1", "-", 1, 1, [42, 43, 44, 45, 46, 47, 48, 49, 50]))
reads.append(Read("chr1", "+", 10, 1, [51, 52, 53, 54, 55]))
reads.append(Read("chr2", "+", 10, 1,
[18, 19, 20, 21, 22, 23, 24, 25]))
# starting count
for count_method in ['all', 'start', 'end']:
print "\nTesting count_method option: ****{}****".format(
count_method)
output = "{}\n".format(feature1)
for r in reads:
output += "{}\n".format(r)
feature1.count_read(r, count_method, count_partial_reads=True)
output += "{}\n".format(feature1)
output += feature1.print_metagene(pretty=True)
if str(feature1.print_metagene()).strip() == str(
expected[method][count_method]).strip():
print "PASSED\tCreated correct metagene with feature method {} and count method {} ?".format(
method, count_method)
else:
print "**FAILED**\tCreated correct metagene with feature method {} and count method {} ?".format(
method, count_method)
print "\tExpected:\n{}".format(expected[method][count_method])
print "\tActual :\n{}".format(feature1.print_metagene())
print "\tSummary of run:\n{}".format(output)
feature1 = Feature.create_from_bed(
method, metagene[method], feature_line, False,
False) # zero out counter for next round
try:
unstranded_read = Read("chr1", ".", 10, 1,
[18, 19, 20, 21, 22, 23, 24, 25])
feature1.count_read(unstranded_read, 'all')
except MetageneError as err:
print "PASSED\tCaught unstranded read on stranded count ?\t\t".format(
err)
else:
print "**FAILED**\tCaught unstranded read on stranded count ?"
try:
feature_line = "{}\t{}\t{}\t{}\t{}\t{}\n".format(
1, 20, 40, "first", 44, ".")
feature1 = Feature.create_from_bed(method, metagene[method],
feature_line, False, False)
unstranded_read = Read("chr1", ".", 10, 1,
[18, 19, 20, 21, 22, 23, 24, 25])
feature1.count_read(unstranded_read, 'all')
except MetageneError as err:
print "**FAILED**\tAllowed unstranded read on unstranded count ?\t\t".format(
err)
else:
print "PASSED\tAllowed unstranded read on unstranded count ?"
print "\n**** Testing adjust_to_metagene ****\n"
chromosome_converter = {"1": "chr1", "2": "chr2"}
# ((metagene_tupple),(feature_tupple),expected_result_string, message_string)
tests = [((8, 2, 2), (16, 8, 24, 4),
'8.000,8.000,4.000,4.000,12.000,12.000,2.000,2.000',
"Expand to metagene ?"),
((4, 2, 2), (6, 8, 6, 2, 4, 4, 2, 4, 24, 8),
'17.000,9.000,8.000,34.000', "Contract to metagene ?"),
((4, 2, 2), (2.5, 4, (10.0 / 3), 10, 11, 7.3, 4),
'5.500,9.333,17.825,9.475', "Contract with messy floats ?"),
((3, 2, 2), (2.5, 4, (10.0 / 3), 10, 11, 7.3, 4),
'7.611,19.556,14.967', "Contract with other messy floats ?")]
for t in tests:
metagene = Metagene(*t[0])
print "\t{}".format(metagene)
feature_line = "{}\t{}\t{}\n".format(1, 0, len(t[1]))
feature = Feature.create_from_bed('all',
metagene,
feature_line,
False,
False,
short=True)
adjusted_feature = ""
for f in feature.adjust_to_metagene(t[1]):
adjusted_feature += "{0:0.3f},".format(f)
if adjusted_feature[:-1] == t[2]:
print "PASSED\t{}".format(t[3])
else:
print "**FAILED**\t{}".format(t[3])
print "\tExpected:\t{}".format(t[2])
print "\tActual :\t{}".format(adjusted_feature[:-1])
print "\tOriginal:\t{}".format(feature.adjust_to_metagene(t[1]))
print "\n**** End of Testing the Feature class ****\n"
# end of Feature.test method
def setup():
"""Create fixtures"""
# Define chromosome sizes
Read.extract_chromosome_sizes(["@HD\tVN:1.0\tSO:unsorted",
"@SQ\tSN:chr1\tLN:300",
"@SQ\tSN:chr2\tLN:200",
"@PG\tID:test\tVN:0.1"])
Feature.process_set_chromosome_conversion(["1\tchr1",
"2\tchr2"])
good_input["bed input counting all of the read"] = ("all",
"[17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]")
good_input["bed input counting start of the read"] = ("start",
"[17, 18, 19, 20, 21, 22, 23]")
good_input["bed input counting end of the read"] = ("end",
"[36, 37, 38, 39, 40, 41, 42]")
good_input["gff input counting all of the read"] = ("all",
"[43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8]")
good_input["gff input counting start of the read"] = ("start",
"[43, 42, 41, 40, 39, 38, 37]")
good_input["gff input counting end of the read"] = ("end",
"[14, 13, 12, 11, 10, 9, 8]")
for method in ['all', 'start', 'end']:
print "\nTesting feature_count option: ****{}****".format(method)
if method == 'all':
metagene = Metagene(10, 4, 2)
print "\t with Metagene:\t{}".format(metagene)
print "\t with chromosome conversions:\t{}".format(Feature.chromosome_conversion)
else:
metagene = Metagene(1, 4, 2)
print "\t with Metagene:\t{}".format(metagene)
print "\t with chromosome conversions:\t{}".format(Feature.chromosome_conversion)
# create feature from BED line
try:
bedline = "{}\t{}\t{}\t{}\t{}\t{}\n".format(1, 20, 40, "first", 44, "+")
print "\t with BED line:\t{}".format(bedline.strip())
feature1 = Feature.create_from_bed(method, metagene, bedline, False, False)
if str(feature1.position_array) != correct_features['bed'][method]:
print "**FAILED**\t Create Feature from BED line ?"
print "\t Desired positions:\t{}".format(correct_features['bed'][method])
print "\t Created positions:\t{}".format(feature1.position_array)
except MetageneError as err:
print "**FAILED**\t Create Feature from BED line ?"
else:
print "PASSED\t Create Feature from BED line ?\t\t{}".format(feature1.get_chromosome_region())
# create feature from GFF line
try:
gffline = "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(2, "test", "gene", 10, 39, ".", "-", ".", "second")
print "\t with GFF line:\t{}".format(gffline.strip())
feature2 = Feature.create_from_gff(method, metagene, gffline, False, False)
if str(feature2.position_array) != correct_features['gff'][method]:
print "**FAILED**\t Create Feature from GFF line ?\t**FAIL**"
print "\t Desired positions:\t{}".format(correct_features['gff'][method])
print "\t Created positions:\t{}".format(feature2.position_array)
except MetageneError as err:
print "**FAILED**\t Create Feature from GFF line ?"
else:
print "PASSED\t Create Feature from GFF line ?\t\t{}".format(feature2.get_chromosome_region())
# create feature from GFF line with start and end swapped
try:
gffline = "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(2, "test", "gene", 39, 10, ".", "-", ".", "second")
print "\t with GFF line:\t{}".format(gffline.strip())
feature2 = Feature.create_from_gff(method, metagene, gffline, False, False)
if str(feature2.position_array) != correct_features['gff'][method]:
print "**FAILED**\t Create Feature from GFF line with swapped start and end ?\t**FAIL**"
print "\t Desired positions:\t{}".format(correct_features['gff'][method])
print "\t Created positions:\t{}".format(feature2.position_array)
except MetageneError as err:
print "**FAILED**\t Create Feature from GFF line with swapped start and end ?"
else:
print "PASSED\t Create Feature from GFF line with swapped start and end ?\t\t{}".format(
feature2.get_chromosome_region())
try:
gffline = "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(2, "test", "gene", 39, 10, ".", "+", ".", "second")
print "\t with GFF line:\t{}".format(gffline.strip())
feature2 = Feature.create_from_gff(method, metagene, gffline, False, False)
if str(feature2.position_array) != correct_features['gff'][method]:
print "**FAILED**\t Do not create Feature from GFF line with swapped start and end, + strand ?\t**FAIL**"
print "\t Desired positions:\t{}".format(correct_features['gff'][method])
print "\t Created positions:\t{}".format(feature2.position_array)
except MetageneError as err:
print "PASSED\t Do not create Feature from GFF line with swapped start and end, + strand ?\t\t{}".format(
err)
else:
print "**FAILED**\t Do not create Feature from GFF line with swapped start and end, + strand ?\t\t{}".format(
feature2.get_chromosome_region())
##TODO finish complete testing of Feature class
print "\n##TODO finish testing of Feature class creation\n"
print "\n**** Testing counting and maniputlation ****\n"
expected = {'all': {}, 'start': {}, 'end': {}}
# Positions in metagene: 17 18 19 20 21-22,23-24,25-26,27-28,29-30,31-32,33-34,35-36,37-38,39-40, 41, 42
expected['all'] = {
'all': "first,sense:allreads,0.333,0.333,0.000,0.000,0.000,0.000,0.000,0.000,0.286,0.571,0.571,0.000,0.000,0.286,0.286,0.000\nfirst,antisense:allreads,0.000,0.000,0.000,0.000,0.000,0.100,0.100,0.100,0.100,0.100,0.000,0.000,0.000,0.000,0.000,0.111",
'start': "first,sense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,2.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000\nfirst,antisense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.500,0.000,0.000,0.000,0.000,0.000,0.000",
'end': "first,sense:allreads,0.000,3.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,2.000,0.000\nfirst,antisense:allreads,0.000,0.000,0.000,0.000,0.000,0.500,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.000,1.000"}
# Positions in metagene: 17 18 19 20 [21] 22 23
expected['start'] = {
'all': "first,sense:allreads,0.333,0.333,0.000,0.000,0.000,0.000,0.000\nfirst,antisense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,0.050",
'start': "first,sense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,0.000\nfirst,antisense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,0.000",
'end': "first,sense:allreads,0.000,3.000,0.000,0.000,0.000,0.000,0.000\nfirst,antisense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,0.500"}
# Positions in metagene: 36 37 38 39 [40] 41 42
expected['end'] = {
'all': "first,sense:allreads,0.000,0.000,0.000,0.000,0.286,0.286,0.000\nfirst,antisense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,0.111",
'start': "first,sense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,0.000\nfirst,antisense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,0.000",
'end': "first,sense:allreads,0.000,0.000,0.000,0.000,0.000,2.000,0.000\nfirst,antisense:allreads,0.000,0.000,0.000,0.000,0.000,0.000,1.000"}
metagene = {'all': Metagene(10, 4, 2),
'start': Metagene(1, 4, 2),
'end': Metagene(1, 4, 2)}
for method in ['all', 'start', 'end']:
if method == 'all':
print "\t with Metagene:\t{}".format(metagene[method])
print "\t with chromosome conversions:\t{}".format(Feature.chromosome_conversion)
else:
print "\t with Metagene:\t{}".format(metagene[method])
print "\t with chromosome conversions:\t{}".format(Feature.chromosome_conversion)
print "\nTesting feature_count option: ****{}****".format(method)
feature_line = "{}\t{}\t{}\t{}\t{}\t{}\n".format(1, 20, 40, "first", 44, "+")
feature1 = Feature.create_from_bed(method, metagene[method], feature_line, False, False)
print "\tFeature:\t{}".format(feature1.position_array)
reads = []
reads.append(Read("chr1", "+", 3, 1, [10, 11, 12, 13, 14, 15, 16, 17, 18]))
reads.append(Read("chr1", "-", 1, 2, [23, 24, 25, 26, 27, 28, 29, 30, 31, 32]))
reads.append(Read("chr1", "+", 4, 2, [30, 31, 32, 33, 34, 40, 41]))
reads.append(Read("chr1", "-", 1, 1, [42, 43, 44, 45, 46, 47, 48, 49, 50]))
reads.append(Read("chr1", "+", 10, 1, [51, 52, 53, 54, 55]))
reads.append(Read("chr2", "+", 10, 1, [18, 19, 20, 21, 22, 23, 24, 25]))
# starting count
for count_method in ['all', 'start', 'end']:
print "\nTesting count_method option: ****{}****".format(count_method)
output = "{}\n".format(feature1)
for r in reads:
output += "{}\n".format(r)
feature1.count_read(r, count_method, count_partial_reads=True)
output += "{}\n".format(feature1)
output += feature1.print_metagene(pretty=True)
if str(feature1.print_metagene()).strip() == str(expected[method][count_method]).strip():
print "PASSED\tCreated correct metagene with feature method {} and count method {} ?".format(method,
count_method)
else:
print "**FAILED**\tCreated correct metagene with feature method {} and count method {} ?".format(method,
count_method)
print "\tExpected:\n{}".format(expected[method][count_method])
print "\tActual :\n{}".format(feature1.print_metagene())
print "\tSummary of run:\n{}".format(output)
feature1 = Feature.create_from_bed(method, metagene[method], feature_line, False,
False) # zero out counter for next round
try:
unstranded_read = Read("chr1", ".", 10, 1, [18, 19, 20, 21, 22, 23, 24, 25])
feature1.count_read(unstranded_read, 'all')
except MetageneError as err:
print "PASSED\tCaught unstranded read on stranded count ?\t\t".format(err)
else:
print "**FAILED**\tCaught unstranded read on stranded count ?"
try:
feature_line = "{}\t{}\t{}\t{}\t{}\t{}\n".format(1, 20, 40, "first", 44, ".")
feature1 = Feature.create_from_bed(method, metagene[method], feature_line, False, False)
unstranded_read = Read("chr1", ".", 10, 1, [18, 19, 20, 21, 22, 23, 24, 25])
feature1.count_read(unstranded_read, 'all')
except MetageneError as err:
print "**FAILED**\tAllowed unstranded read on unstranded count ?\t\t".format(err)
else:
print "PASSED\tAllowed unstranded read on unstranded count ?"
print "\n**** Testing adjust_to_metagene ****\n"
chromosome_converter = {"1": "chr1", "2": "chr2"}
# ((metagene_tupple),(feature_tupple),expected_result_string, message_string)
tests = [((8, 2, 2), (16, 8, 24, 4), '8.000,8.000,4.000,4.000,12.000,12.000,2.000,2.000', "Expand to metagene ?"),
((4, 2, 2), (6, 8, 6, 2, 4, 4, 2, 4, 24, 8), '17.000,9.000,8.000,34.000', "Contract to metagene ?"),
((4, 2, 2), (2.5, 4, (10.0 / 3), 10, 11, 7.3, 4), '5.500,9.333,17.825,9.475',
"Contract with messy floats ?"),
((3, 2, 2), (2.5, 4, (10.0 / 3), 10, 11, 7.3, 4), '7.611,19.556,14.967',
"Contract with other messy floats ?")]
for t in tests:
metagene = Metagene(*t[0])
print "\t{}".format(metagene)
feature_line = "{}\t{}\t{}\n".format(1, 0, len(t[1]))
feature = Feature.create_from_bed('all', metagene, feature_line, False, False, short=True)
adjusted_feature = ""
for f in feature.adjust_to_metagene(t[1]):
adjusted_feature += "{0:0.3f},".format(f)
if adjusted_feature[:-1] == t[2]:
print "PASSED\t{}".format(t[3])
else:
print "**FAILED**\t{}".format(t[3])
print "\tExpected:\t{}".format(t[2])
print "\tActual :\t{}".format(adjusted_feature[:-1])
print "\tOriginal:\t{}".format(feature.adjust_to_metagene(t[1]))
print "\n**** End of Testing the Feature class ****\n"
# end of Feature.test method
