def test_convert_to_mRNA_position_fail(self):
""" Various attempts to break RNA position and make sure that error are caught """
return
tool = pybedtools.create_interval_from_list(
"ENSMUSG1 51 60 ENSMUSG1_1_83;ENSMUSG1_6_83 0 - 10 10"
.split())
location_dict = {
"ENSMUSG1": {
"strand": "-",
"regions": [
(100, 150),
(25, 50),
]
}
}
self.assertEqual(
convert_to_mRNA_position(tool, location_dict).chrom, "none")
tool = pybedtools.create_interval_from_list(
"ENSMUSG1 51 60 ENSMUSG1_1_83;ENSMUSG1_6_83 0 - 175 175"
.split())
self.assertEqual(
convert_to_mRNA_position(tool, location_dict).chrom, "none")
pybedtools.BedTool("chr1 x y ")
def test_convert_to_mRNA_position_placement_split(self):
"""
Makes sure that lists of regions works for both positive and negative strands
"""
return
tool = pybedtools.create_interval_from_list("ENSMUSG1 125 127 ENSMUSG1_1_83;ENSMUSG1_6_83 0 + 125 125".split())
location_dict = {"ENSMUSG1" : {"strand" : "+", "regions" : [(0, 50),
(100, 150),
]
}
}
correct_tool = pybedtools.create_interval_from_list("ENSMUSG1 75 77 ENSMUSG1_1_83;ENSMUSG1_6_83 0 + 125 125".split())
self.assertEqual(convert_to_mRNA_position(tool, location_dict), correct_tool )
tool = pybedtools.create_interval_from_list("ENSMUSG1 25 27 ENSMUSG1_1_83;ENSMUSG1_6_83 0 - 25 25".split())
location_dict = {"ENSMUSG1" : {"strand" : "-", "regions" : [(100, 150),
(0, 50),
]
}
}
correct_tool = pybedtools.create_interval_from_list("ENSMUSG1 73 75 ENSMUSG1_1_83;ENSMUSG1_6_83 0 - 25 25".split())
self.assertEqual(convert_to_mRNA_position(tool, location_dict), correct_tool)
def test_convert_to_mRNA_position_placement(self):
"""
Makes sure that the placement within a region or list of regions is correct
"""
return
interval = pybedtools.create_interval_from_list("ENSMUSG1 50 60 ENSMUSG1_1_83;ENSMUSG1_6_83 0 + 60 60".split())
location_dict = {"ENSMUSG1" : {"strand" : "+", "regions" : [(0,100),
]
}
}
correct_tool = pybedtools.create_interval_from_list("ENSMUSG1 50 60 ENSMUSG1_1_83;ENSMUSG1_6_83 0 + 60 60".split())
self.assertEqual(convert_to_mRNA_position(interval, location_dict), correct_tool)
interval = pybedtools.create_interval_from_list("ENSMUSG1 50 60 ENSMUSG1_1_83;ENSMUSG1_6_83 0 -".split())
location_dict = {"ENSMUSG1" : {"strand" : "-", "regions" : [(0,100),
]
}
}
#individual_fraction, total_fraction
correct_tool = pybedtools.create_interval_from_list("ENSMUSG1 40 50 ENSMUSG1_1_83;ENSMUSG1_6_83 0 -".split())
x = convert_to_mRNA_position(interval, location_dict)
print x
self.assertEqual(x, correct_tool)
def test_convert_to_mRNA_position_placement_split(self):
"""
Makes sure that lists of regions works for both positive and negative strands
"""
return
tool = pybedtools.create_interval_from_list(
"ENSMUSG1 125 127 ENSMUSG1_1_83;ENSMUSG1_6_83 0 + 125 125"
.split())
location_dict = {
"ENSMUSG1": {
"strand": "+",
"regions": [
(0, 50),
(100, 150),
]
}
}
correct_tool = pybedtools.create_interval_from_list(
"ENSMUSG1 75 77 ENSMUSG1_1_83;ENSMUSG1_6_83 0 + 125 125"
.split())
self.assertEqual(convert_to_mRNA_position(tool, location_dict),
correct_tool)
tool = pybedtools.create_interval_from_list(
"ENSMUSG1 25 27 ENSMUSG1_1_83;ENSMUSG1_6_83 0 - 25 25"
.split())
location_dict = {
"ENSMUSG1": {
"strand": "-",
"regions": [
(100, 150),
(0, 50),
]
}
}
correct_tool = pybedtools.create_interval_from_list(
"ENSMUSG1 73 75 ENSMUSG1_1_83;ENSMUSG1_6_83 0 - 25 25"
.split())
self.assertEqual(convert_to_mRNA_position(tool, location_dict),
correct_tool)
def test_convert_to_mRNA_position_placement(self):
"""
Makes sure that the placement within a region or list of regions is correct
"""
return
interval = pybedtools.create_interval_from_list(
"ENSMUSG1 50 60 ENSMUSG1_1_83;ENSMUSG1_6_83 0 + 60 60"
.split())
location_dict = {
"ENSMUSG1": {
"strand": "+",
"regions": [
(0, 100),
]
}
}
correct_tool = pybedtools.create_interval_from_list(
"ENSMUSG1 50 60 ENSMUSG1_1_83;ENSMUSG1_6_83 0 + 60 60"
.split())
self.assertEqual(convert_to_mRNA_position(interval, location_dict),
correct_tool)
interval = pybedtools.create_interval_from_list(
"ENSMUSG1 50 60 ENSMUSG1_1_83;ENSMUSG1_6_83 0 -".
split())
location_dict = {
"ENSMUSG1": {
"strand": "-",
"regions": [
(0, 100),
]
}
}
#individual_fraction, total_fraction
correct_tool = pybedtools.create_interval_from_list(
"ENSMUSG1 40 50 ENSMUSG1_1_83;ENSMUSG1_6_83 0 -".
split())
x = convert_to_mRNA_position(interval, location_dict)
print x
self.assertEqual(x, correct_tool)
def test_convert_to_mRNA_position_fail(self):
""" Various attempts to break RNA position and make sure that error are caught """
return
tool = pybedtools.create_interval_from_list("ENSMUSG1 51 60 ENSMUSG1_1_83;ENSMUSG1_6_83 0 - 10 10".split())
location_dict = {"ENSMUSG1" : {"strand" : "-", "regions" : [(100, 150),
(25,50),
]
}
}
self.assertEqual(convert_to_mRNA_position(tool, location_dict).chrom, "none")
tool = pybedtools.create_interval_from_list("ENSMUSG1 51 60 ENSMUSG1_1_83;ENSMUSG1_6_83 0 - 175 175".split())
self.assertEqual(convert_to_mRNA_position(tool, location_dict).chrom, "none")
pybedtools.BedTool("chr1 x y ")