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from unittest import TestCase
from cogent3.util.table import Table
class FormatBedgraph(TestCase):
def test_only_required_columns(self):
"""generate bedgraph from minimal data"""
table = Table(
header=["chrom", "start", "end", "value"],
data=[["1", 100, i, 0] for i in range(101, 111)]
+ [["1", 150, i, 10] for i in range(151, 161)],
)
bgraph = table.to_string(
format="bedgraph",
name="test track",
description="test of bedgraph",
color=(255, 0, 0),
)
self.assertTrue(
bgraph,
"\n".join(
[
'track type=bedGraph name="test track" '
+ 'description="test of bedgraph" color=255,0,0',
"1\t100\t110\t0",
"1\t150\t160\t10",
]
),
)
def test_merged_overlapping_spans(self):
"""bedgraph merged overlapping spans, one chrom"""
rows = [["1", i, i + 1, 0] for i in range(100, 121)] + [
["1", i, i + 1, 10] for i in range(150, 161)
]
table = Table(header=["chrom", "start", "end", "value"], data=rows)
bgraph = table.to_string(
format="bedgraph",
name="test track",
description="test of bedgraph",
color=(255, 0, 0),
)
self.assertTrue(
bgraph,
"\n".join(
[
'track type=bedGraph name="test track" '
+ 'description="test of bedgraph" color=255,0,0',
"1\t100\t120\t0",
"1\t150\t160\t10",
]
),
)
def test_merged_overlapping_spans_multichrom(self):
"""bedgraph merged overlapping spans, two crhoms"""
rows = [["1", i, i + 1, 0] for i in range(100, 121)] + [
["1", i, i + 1, 10] for i in range(150, 161)
]
rows += [["2", i, i + 1, 0] for i in range(100, 121)]
table = Table(header=["chrom", "start", "end", "value"], data=rows)
bgraph = table.to_string(
format="bedgraph",
name="test track",
description="test of bedgraph",
color=(255, 0, 0),
)
self.assertTrue(
bgraph,
"\n".join(
[
'track type=bedGraph name="test track" '
+ 'description="test of bedgraph" color=255,0,0',
"1\t100\t120\t1",
"1\t150\t160\t10",
"2\t105\t120\t1",
]
),
)
def test_invalid_args_fail(self):
"""incorrect bedgraph args causes RuntimeError"""
rows = [["1", i, i + 1, 0] for i in range(100, 121)] + [
["1", i, i + 1, 10] for i in range(150, 161)
]
table = Table(header=["chrom", "start", "end", "value"], data=rows)
self.assertRaises(
RuntimeError,
table.to_string,
format="bedgraph",
name="test track",
description="test of bedgraph",
color=(255, 0, 0),
abc=None,
)
def test_invalid_table_fails(self):
"""assertion error if table has > 4 columns"""
rows = [["1", i, i + 1, 0, 1] for i in range(100, 121)] + [
["1", i, i + 1, 10, 1] for i in range(150, 161)
]
table = Table(header=["chrom", "start", "end", "value", "blah"], data=rows)
self.assertRaises(
AssertionError,
table.to_string,
format="bedgraph",
name="test track",
description="test of bedgraph",
color=(255, 0, 0),
abc=None,
)
def test_boolean_correctly_formatted(self):
"""boolean setting correctly formatted"""
rows = [["1", i, i + 1, 0] for i in range(100, 121)] + [
["1", i, i + 1, 10] for i in range(150, 161)
]
table = Table(header=["chrom", "start", "end", "value"], data=rows)
bgraph = table.to_string(
format="bedgraph",
name="test track",
description="test of bedgraph",
color=(255, 0, 0),
autoScale=True,
)
self.assertTrue(
bgraph,
"\n".join(
[
'track type=bedGraph name="test track" '
+ 'description="test of bedgraph" color=255,0,0 autoScale=on',
"1\t100\t110\t1",
"1\t150\t160\t10",
]
),
)
def test_int_correctly_formatted(self):
"""int should be correctly formatted"""
rows = [["1", i, i + 1, 0] for i in range(100, 121)] + [
["1", i, i + 1, 10] for i in range(150, 161)
]
table = Table(header=["chrom", "start", "end", "value"], data=rows)
bgraph = table.to_string(
format="bedgraph",
name="test track",
description="test of bedgraph",
color=(255, 0, 0),
smoothingWindow=10,
)
self.assertTrue(
bgraph,
"\n".join(
[
'track type=bedGraph name="test track" '
+ 'description="test of bedgraph" color=255,0,0 smoothingWindow=10',
"1\t100\t110\t1",
"1\t150\t160\t10",
]
),
)
def test_raises_on_incorrect_format_val(self):
"""raise AssertionError when provide incorrect format value"""
rows = [["1", i, i + 1, 0] for i in range(100, 121)] + [
["1", i, i + 1, 10] for i in range(150, 161)
]
table = Table(header=["chrom", "start", "end", "value"], data=rows)
self.assertRaises(
AssertionError,
table.to_string,
format="bedgraph",
name="test track",
description="test of bedgraph",
color=(255, 0, 0),
windowingFunction="sqrt",
)
|
