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"""
Tests for `bx.wiggle`.
"""
import unittest
from io import StringIO
from bx import wiggle
# A modified version of UCSC's example wiggle, taken from http://genome.ucsc.edu/goldenPath/help/wiggleExample.txt
test_wig = """browser position chr19:59302001-59311000
browser hide all
browser pack refGene encodeRegions
browser full altGraph
# 5 base wide bar graph, autoScale is on by default == graphing
# limits will dynamically change to always show full range of data
# in viewing window, priority = 20 positions this as the second graph
# Note, zero-relative, half-open coordinate system in use for bed format
track type=wiggle_0 name="Bed Format" description="BED format" visibility=full color=200,100,0 altColor=0,100,200 priority=20
chr19 59302000 59302005 -1.0
chr19 59302300 59302305 -0.75
# 4 base wide bar graph at arbitrarily spaced positions,
# threshold line drawn at y=11.76
# autoScale off viewing range set to [0:25]
# priority = 10 positions this as the first graph
# Note, one-relative coordinate system in use for this format
track type=wiggle_0 name="variableStep" description="variableStep format" visibility=full autoScale=off viewLimits=0.0:25.0 color=255,200,0 yLineMark=11.76 yLineOnOff=on priority=10
variableStep chrom=chr19 span=4
59304701 10.0
59304901 12.5
# 3 base wide points graph at every 300 bases, 50 pixel high graph
# autoScale off and viewing range set to [0:1000]
# priority = 30 positions this as the third graph
# Note, one-relative coordinate system in use for this format
track type=wiggle_0 name="fixedStep" description="fixed step" visibility=full autoScale=off viewLimits=0:1000 color=0,200,100 maxHeightPixels=100:50:20 graphType=points priority=30
fixedStep chrom=chr19 start=59307401 step=300 span=3
1000
900
800
"""
interval_reader_result = [
"chr19,59302000,59302005,+,-1.0",
"chr19,59302300,59302305,+,-0.75",
"chr19,59304700,59304704,+,10.0",
"chr19,59304900,59304904,+,12.5",
"chr19,59307400,59307403,+,1000.0",
"chr19,59307700,59307703,+,900.0",
"chr19,59308000,59308003,+,800.0",
]
position_reader_result = [
"chr19,59302000,-1.0",
"chr19,59302001,-1.0",
"chr19,59302002,-1.0",
"chr19,59302003,-1.0",
"chr19,59302004,-1.0",
"chr19,59302300,-0.75",
"chr19,59302301,-0.75",
"chr19,59302302,-0.75",
"chr19,59302303,-0.75",
"chr19,59302304,-0.75",
"chr19,59304700,10.0",
"chr19,59304701,10.0",
"chr19,59304702,10.0",
"chr19,59304703,10.0",
"chr19,59304900,12.5",
"chr19,59304901,12.5",
"chr19,59304902,12.5",
"chr19,59304903,12.5",
"chr19,59307400,1000.0",
"chr19,59307401,1000.0",
"chr19,59307402,1000.0",
"chr19,59307700,900.0",
"chr19,59307701,900.0",
"chr19,59307702,900.0",
"chr19,59308000,800.0",
"chr19,59308001,800.0",
"chr19,59308002,800.0",
]
class TestWiggleReader(unittest.TestCase):
def test_reader(self):
# Test position reader
assert position_reader_result == [",".join(map(str, value)) for value in wiggle.Reader(StringIO(test_wig))]
def test_interval_reader(self):
# Test interval reader reader
assert interval_reader_result == [
",".join(map(str, value)) for value in wiggle.IntervalReader(StringIO(test_wig))
]
if __name__ == "__main__":
unittest.main()
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