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1271 lines (1031 loc) · 51.1 KB
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import unittest
import sys
sys.path.append('../../src/')
import samplot
bam_1 = '../data/NA12878_restricted.bam'
bam_2 = '../data/NA12889_restricted.bam'
bam_3 = '../data/NA12890_restricted.bam'
bams=[bam_1, bam_2, bam_3]
sv_chrm = 'chr4'
sv_start = 115928730
sv_end = 115931875
sv_type = 'DEL'
#{{{ class Test_set_plot_dimensions(unittest.TestCase):
class Test_set_plot_dimensions(unittest.TestCase):
#{{{ def test_set_plot_dimensions(self):
def test_set_plot_dimensions(self):
'''
def set_plot_dimensions(sv,
sv_type,
arg_plot_height,
arg_plot_width,
bams,
annotation_files,
transcript_file,
arg_window,
zoom):
'''
plot_height = None
plot_width = None
annotation_files = None
transcript_file = None
zoom = None
window = None
sv = [samplot.genome_interval(sv_chrm,sv_start,sv_end)]
# Test basic function where window is set to be proportional to SV size
r_plot_height, r_plot_width, r_window, r_ranges = \
samplot.set_plot_dimensions(sv,
sv_type,
plot_height,
plot_width,
bams,
annotation_files,
transcript_file,
window,
zoom)
self.assertEqual(r_plot_height, 5)
self.assertEqual(r_plot_width, 8)
this_window = int((sv_end - sv_start)/2)
self.assertEqual( r_window, this_window)
self.assertEqual( r_ranges[0],
samplot.genome_interval(sv_chrm,
sv_start - this_window,
sv_end + this_window))
# Test to see if zoom is ignored when it is larger than window
zoom = 10000
r_plot_height, r_plot_width, r_window, r_ranges = \
samplot.set_plot_dimensions(sv,
sv_type,
plot_height,
plot_width,
bams,
annotation_files,
transcript_file,
window,
zoom)
self.assertEqual( r_ranges[0],
samplot.genome_interval(sv_chrm,
sv_start - this_window,
sv_end + this_window))
# Test to see if zoom creates two ranges
zoom = 100
r_plot_height, r_plot_width, r_window, r_ranges = \
samplot.set_plot_dimensions(sv,
sv_type,
plot_height,
plot_width,
bams,
annotation_files,
transcript_file,
window,
zoom)
self.assertEqual( r_window, zoom)
self.assertEqual( len(r_ranges), 2)
self.assertEqual( r_ranges[0],
samplot.genome_interval(sv_chrm,
sv_start - zoom,
sv_start + zoom,))
self.assertEqual( r_ranges[1],
samplot.genome_interval(sv_chrm,
sv_end - zoom,
sv_end + zoom) )
# Test to multiple sv regions
window = None
zoom = None
sv = [samplot.genome_interval(sv_chrm,sv_start,sv_start),
samplot.genome_interval(sv_chrm,sv_end,sv_end)]
r_plot_height, r_plot_width, r_window, r_ranges = \
samplot.set_plot_dimensions(sv,
sv_type,
plot_height,
plot_width,
bams,
annotation_files,
transcript_file,
window,
zoom)
self.assertEqual( len(r_ranges), 2)
self.assertEqual( r_ranges[0],
samplot.genome_interval(sv_chrm,
sv_start-1000,
sv_start+1000) )
self.assertEqual( r_ranges[1],
samplot.genome_interval(sv_chrm,
sv_end-1000,
sv_end+1000) )
#}}}
#{{{def test_get_read_data(self):
def test_get_read_data(self):
'''
read_data,max_coverage = get_read_data(ranges,
options.bams,
options.reference,
options.min_mqual,
options.coverage_only,
options.long_read,
options.same_yaxis_scales,
options.max_depth,
options.z)
'''
plot_height = None
plot_width = None
annotation_files = None
transcript_file = None
zoom = None
window = None
sv = [samplot.genome_interval(sv_chrm,sv_start,sv_end)]
# Test basic function where window is set to be proportional to SV size
r_plot_height, r_plot_width, r_window, r_ranges = \
samplot.set_plot_dimensions(sv,
sv_type,
plot_height,
plot_width,
bams,
annotation_files,
transcript_file,
window,
zoom)
reference = None
min_mqual = None
coverage_only = None
long_read = 1000
long_even_size = 100
same_yaxis_scales = None
max_depth = 100
z = 4
read_data,max_coverage = samplot.get_read_data(r_ranges,
bams,
reference,
min_mqual,
coverage_only,
long_read,
long_even_size,
same_yaxis_scales,
max_depth,
z)
#}}}
#}}}
#{{{ class Test_genome_interval(unittest.TestCase):
class Test_genome_interval(unittest.TestCase):
#{{{ def test_init(self):
def test_init(self):
gi = samplot.genome_interval('chr1', 1, 1000)
self.assertEqual(gi.chrm, 'chr1')
self.assertEqual(gi.start, 1)
self.assertEqual(gi.end, 1000)
#}}}
#{{{ def test_init(self):
def test_intersect(self):
gi = samplot.genome_interval('chr8', 500, 1000)
self.assertEqual(-1,
gi.intersect(samplot.genome_interval('chr7',
500,
1000)))
self.assertEqual(1,
gi.intersect(samplot.genome_interval('chr9',
500,
1000)))
self.assertEqual(-1,
gi.intersect(samplot.genome_interval('chr8',
100,
499)))
self.assertEqual(1,
gi.intersect(samplot.genome_interval('chr8',
1001,
2000)))
self.assertEqual(0,
gi.intersect(samplot.genome_interval('chr8',
1,
500)))
self.assertEqual(0,
gi.intersect(samplot.genome_interval('chr8',
500,
501)))
self.assertEqual(0,
gi.intersect(samplot.genome_interval('chr8',
1000,
2000)))
#}}}
#{{{ def test_get_range_hit(self):
def test_get_range_hit(self):
gi_0 = samplot.genome_interval('chr8', 500, 1000)
ranges = [gi_0]
self.assertEqual(0, samplot.get_range_hit(ranges, 'chr8', 500))
gi_1 = samplot.genome_interval('chr8', 2000, 3000)
ranges = [gi_0, gi_1]
self.assertEqual(0, samplot.get_range_hit(ranges, 'chr8', 500))
self.assertEqual(1, samplot.get_range_hit(ranges, 'chr8', 2500))
self.assertEqual(None, samplot.get_range_hit(ranges, 'chr7', 2500))
self.assertEqual(None, samplot.get_range_hit(ranges, 'chr8', 100))
self.assertEqual(None, samplot.get_range_hit(ranges, 'chr8', 10000))
#}}}
#{{{ def test_map_genome_point_to_range_points(self):
def test_map_genome_point_to_range_points(self):
gi_0 = samplot.genome_interval('chr8', 100, 200)
ranges = [gi_0]
self.assertEqual(None,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
10))
self.assertEqual(0.0,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
100))
self.assertEqual(0.25,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
125))
self.assertEqual(0.5,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
150))
self.assertEqual(0.75,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
175))
self.assertEqual(1.0,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
200))
self.assertEqual(None,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
201))
gi_1 = samplot.genome_interval('chr8', 300, 400)
ranges = [gi_0, gi_1]
self.assertEqual(None,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
10))
self.assertEqual(0.0,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
100))
self.assertEqual(0.25/2,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
125))
self.assertEqual(0.5/2,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
150))
self.assertEqual(0.75/2,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
175))
self.assertEqual(1.0/2,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
200))
self.assertEqual(None,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
201))
self.assertEqual(0.5,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
300))
self.assertEqual(0.5+0.25/2,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
325))
self.assertEqual(0.5+0.5/2,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
350))
self.assertEqual(0.5+0.75/2,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
375))
self.assertEqual(1.0,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
400))
gi_0 = samplot.genome_interval('chr8', 100, 200)
gi_1 = samplot.genome_interval('chr9', 300, 400)
ranges = [gi_0, gi_1]
self.assertEqual(None,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
10))
self.assertEqual(0.0,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
100))
self.assertEqual(0.25/2,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
125))
self.assertEqual(0.5/2,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
150))
self.assertEqual(0.75/2,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
175))
self.assertEqual(1.0/2,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
200))
self.assertEqual(None,
samplot.map_genome_point_to_range_points(ranges,
'chr8',
201))
self.assertEqual(0.5,
samplot.map_genome_point_to_range_points(ranges,
'chr9',
300))
self.assertEqual(0.5+0.25/2,
samplot.map_genome_point_to_range_points(ranges,
'chr9',
325))
self.assertEqual(0.5+0.5/2,
samplot.map_genome_point_to_range_points(ranges,
'chr9',
350))
self.assertEqual(0.5+0.75/2,
samplot.map_genome_point_to_range_points(ranges,
'chr9',
375))
self.assertEqual(1.0,
samplot.map_genome_point_to_range_points(ranges,
'chr9',
400))
#}}}
#}}}
#{{{ class Test_long_read_plan(unittest.TestCase):
class Test_long_read_plan(unittest.TestCase):
#{{{ def test_init(self):
def test_add_align_step(self):
alignment = samplot.Alignment('chr8', 100, 500, True, 0)
# both are in the same range
gi_0 = samplot.genome_interval('chr8', 100, 1000)
ranges = [gi_0]
steps = []
samplot.add_align_step(alignment, steps, ranges)
self.assertEqual(1, len(steps))
self.assertEqual('chr8', steps[0].start_pos.chrm)
self.assertEqual(100, steps[0].start_pos.start)
self.assertEqual(100, steps[0].start_pos.end)
self.assertEqual('chr8', steps[0].end_pos.chrm)
self.assertEqual(500, steps[0].end_pos.start)
self.assertEqual(500, steps[0].end_pos.end)
self.assertEqual('Align', steps[0].info['TYPE'])
# in different ranges
gi_0 = samplot.genome_interval('chr8', 100, 200)
gi_1 = samplot.genome_interval('chr8', 300, 1000)
ranges = [gi_0, gi_1]
steps = []
samplot.add_align_step(alignment, steps, ranges)
self.assertEqual(2, len(steps))
#start
self.assertEqual('chr8', steps[0].start_pos.chrm)
self.assertEqual(100, steps[0].start_pos.start)
self.assertEqual(100, steps[0].start_pos.end)
#end
self.assertEqual('chr8', steps[0].end_pos.chrm)
self.assertEqual(200, steps[0].end_pos.start)
self.assertEqual(200, steps[0].end_pos.end)
#event
self.assertEqual('Align', steps[0].info['TYPE'])
#start
self.assertEqual('chr8', steps[1].start_pos.chrm)
self.assertEqual(300, steps[1].start_pos.start)
self.assertEqual(300, steps[1].start_pos.end)
#end
self.assertEqual('chr8', steps[1].end_pos.chrm)
self.assertEqual(500, steps[1].end_pos.start)
self.assertEqual(500, steps[1].end_pos.end)
#event
self.assertEqual('Align', steps[1].info['TYPE'])
# start is not in range, use end hit
gi_0 = samplot.genome_interval('chr8', 10, 20)
gi_1 = samplot.genome_interval('chr8', 300, 1000)
ranges = [gi_0, gi_1]
steps = []
samplot.add_align_step(alignment, steps, ranges)
self.assertEqual(1, len(steps))
#start
self.assertEqual('chr8', steps[0].start_pos.chrm)
self.assertEqual(300, steps[0].start_pos.start)
self.assertEqual(300, steps[0].start_pos.end)
#end
self.assertEqual('chr8', steps[0].end_pos.chrm)
self.assertEqual(500, steps[0].end_pos.start)
self.assertEqual(500, steps[0].end_pos.end)
#event
self.assertEqual('Align', steps[0].info['TYPE'])
# end is not in range, use start hit
gi_0 = samplot.genome_interval('chr8', 100, 200)
gi_1 = samplot.genome_interval('chr8', 3000, 4000)
ranges = [gi_0, gi_1]
steps = []
samplot.add_align_step(alignment, steps, ranges)
#start
self.assertEqual(1, len(steps))
self.assertEqual('chr8', steps[0].start_pos.chrm)
self.assertEqual(100, steps[0].start_pos.start)
self.assertEqual(100, steps[0].start_pos.end)
#end
self.assertEqual('chr8', steps[0].end_pos.chrm)
self.assertEqual(200, steps[0].end_pos.end)
self.assertEqual(200, steps[0].end_pos.start)
#event
self.assertEqual('Align', steps[0].info['TYPE'])
# neither end is in range, add nothing
gi_0 = samplot.genome_interval('chr8', 10, 20)
gi_1 = samplot.genome_interval('chr8', 3000, 4000)
ranges = [gi_0, gi_1]
steps = []
samplot.add_align_step(alignment, steps, ranges)
self.assertEqual(0, len(steps))
#}}}
#{{{def test_get_alignments_from_cigar(self):
def test_get_alignments_from_cigar(self):
'''
alignments = get_alignments_from_cigar(
bam_file.get_reference_name(read.reference_id),
read.pos,
not read.is_reverse,
read.cigartuples)
'''
CIGAR_MAP = { 'M' : 0,
'I' : 1,
'D' : 2,
'N' : 3,
'S' : 4,
'H' : 5,
'P' : 6,
'=' : 7,
'X' : 8,
'B' : 9 }
cigar = [(CIGAR_MAP['M'], 100),
(CIGAR_MAP['D'], 100),
(CIGAR_MAP['M'], 100)]
alignments = samplot.get_alignments_from_cigar('chr8',
100,
True,
cigar)
self.assertEqual(2,len(alignments))
self.assertEqual('chr8', alignments[0].pos.chrm)
self.assertEqual(100, alignments[0].pos.start)
self.assertEqual(200, alignments[0].pos.end)
self.assertEqual(True, alignments[0].strand)
self.assertEqual(0, alignments[0].query_position)
self.assertEqual('chr8', alignments[1].pos.chrm)
self.assertEqual(300, alignments[1].pos.start)
self.assertEqual(400, alignments[1].pos.end)
self.assertEqual(True, alignments[1].strand)
self.assertEqual(100, alignments[1].query_position)
#}}}
#{{{def test_get_long_read_plan(self):
def test_get_long_read_plan(self):
gi_0 = samplot.genome_interval('chr8', 100, 250)
gi_1 = samplot.genome_interval('chr8', 300, 400)
ranges = [gi_0, gi_1]
long_reads = {}
read_name = 'Test'
alignments = [samplot.Alignment('chr8', 100, 200, True, 0)]
long_reads[read_name] = [ samplot.LongRead(alignments) ]
max_gap, steps = samplot.get_long_read_plan(read_name,
long_reads,
ranges)
self.assertEqual(0, max_gap)
self.assertEqual(1, len(steps))
self.assertEqual('chr8', steps[0].start_pos.chrm)
self.assertEqual(100, steps[0].start_pos.start)
self.assertEqual(100, steps[0].start_pos.end)
self.assertEqual('chr8', steps[0].end_pos.chrm)
self.assertEqual(200, steps[0].end_pos.start)
self.assertEqual(200, steps[0].end_pos.end)
self.assertEqual('LONGREAD', steps[0].event)
self.assertEqual('Align', steps[0].info['TYPE'])
alignments = [samplot.Alignment('chr8', 100, 299, True, 0)]
long_reads[read_name] = [ samplot.LongRead(alignments) ]
max_gap, steps = samplot.get_long_read_plan(read_name,
long_reads,
ranges)
self.assertEqual(0, max_gap)
self.assertEqual(1, len(steps))
self.assertEqual('chr8', steps[0].start_pos.chrm)
self.assertEqual(100, steps[0].start_pos.start)
self.assertEqual(100, steps[0].start_pos.end)
self.assertEqual('chr8', steps[0].end_pos.chrm)
self.assertEqual(250, steps[0].end_pos.start)
self.assertEqual(250, steps[0].end_pos.end)
self.assertEqual('Align', steps[0].info['TYPE'])
alignments = [samplot.Alignment('chr8', 100, 350, True, 0)]
long_reads[read_name] = [ samplot.LongRead(alignments) ]
max_gap, steps = samplot.get_long_read_plan(read_name,
long_reads,
ranges)
self.assertEqual(0, max_gap)
self.assertEqual(2, len(steps))
self.assertEqual('chr8', steps[0].start_pos.chrm)
self.assertEqual(100, steps[0].start_pos.start)
self.assertEqual(100, steps[0].start_pos.end)
self.assertEqual('chr8', steps[0].end_pos.chrm)
self.assertEqual(250, steps[0].end_pos.start)
self.assertEqual(250, steps[0].end_pos.end)
self.assertEqual('Align', steps[0].info['TYPE'])
self.assertEqual('chr8', steps[1].start_pos.chrm)
self.assertEqual(300, steps[1].start_pos.start)
self.assertEqual(300, steps[1].start_pos.end)
self.assertEqual('chr8', steps[1].end_pos.chrm)
self.assertEqual(350, steps[1].end_pos.start)
self.assertEqual(350, steps[1].end_pos.end)
self.assertEqual('Align', steps[1].info['TYPE'])
alignments = [samplot.Alignment('chr8', 100, 250, True, 0),
samplot.Alignment('chr8', 300, 350, True, 150)]
long_reads[read_name] = [ samplot.LongRead(alignments) ]
max_gap, steps = samplot.get_long_read_plan(read_name,
long_reads,
ranges)
self.assertEqual(50, max_gap)
self.assertEqual(3, len(steps))
self.assertEqual('chr8', steps[0].start_pos.chrm)
self.assertEqual(100, steps[0].start_pos.start)
self.assertEqual(100, steps[0].start_pos.end)
self.assertEqual('chr8', steps[0].end_pos.chrm)
self.assertEqual(250, steps[0].end_pos.start)
self.assertEqual(250, steps[0].end_pos.end)
self.assertEqual('Align', steps[0].info['TYPE'])
self.assertEqual('chr8', steps[1].start_pos.chrm)
self.assertEqual(250, steps[1].start_pos.start)
self.assertEqual(250, steps[1].start_pos.end)
self.assertEqual('chr8', steps[1].end_pos.chrm)
self.assertEqual(300, steps[1].end_pos.start)
self.assertEqual(300, steps[1].end_pos.end)
self.assertEqual('Deletion', steps[1].info['TYPE'])
self.assertEqual('chr8', steps[2].start_pos.chrm)
self.assertEqual(300, steps[2].start_pos.start)
self.assertEqual(300, steps[2].start_pos.end)
self.assertEqual('chr8', steps[2].end_pos.chrm)
self.assertEqual(350, steps[2].end_pos.start)
self.assertEqual(350, steps[2].end_pos.end)
self.assertEqual('Align', steps[2].info['TYPE'])
gi_0 = samplot.genome_interval('chr8', 100, 250)
gi_1 = samplot.genome_interval('chr9', 300, 400)
ranges = [gi_0, gi_1]
alignments = [samplot.Alignment('chr8', 100, 250, True, 0),
samplot.Alignment('chr9', 300, 350, True, 150)]
long_reads[read_name] = [ samplot.LongRead(alignments) ]
max_gap, steps = samplot.get_long_read_plan(read_name,
long_reads,
ranges)
self.assertEqual(5000, max_gap)
self.assertEqual(3, len(steps))
self.assertEqual('chr8', steps[0].start_pos.chrm)
self.assertEqual(100, steps[0].start_pos.start)
self.assertEqual(100, steps[0].start_pos.end)
self.assertEqual('chr8', steps[0].end_pos.chrm)
self.assertEqual(250, steps[0].end_pos.start)
self.assertEqual(250, steps[0].end_pos.end)
self.assertEqual('Align', steps[0].info['TYPE'])
self.assertEqual('chr8', steps[1].start_pos.chrm)
self.assertEqual(250, steps[1].start_pos.start)
self.assertEqual(250, steps[1].start_pos.end)
self.assertEqual('chr9', steps[1].end_pos.chrm)
self.assertEqual(300, steps[1].end_pos.start)
self.assertEqual(300, steps[1].end_pos.end)
self.assertEqual('InterChrm', steps[1].info['TYPE'])
self.assertEqual('chr9', steps[2].start_pos.chrm)
self.assertEqual(300, steps[2].start_pos.start)
self.assertEqual(300, steps[2].start_pos.end)
self.assertEqual('chr9', steps[2].end_pos.chrm)
self.assertEqual(350, steps[2].end_pos.start)
self.assertEqual(350, steps[2].end_pos.end)
self.assertEqual('Align', steps[2].info['TYPE'])
#}}}
#}}}
#{{{class Test_annotation_plan(unittest.TestCase):
class Test_annotation_plan(unittest.TestCase):
#{{{def test_get_alignments_from_cigar(self):
def test_get_alignments_from_cigar(self):
gi_1 = samplot.genome_interval('chr8', 100, 200)
gi_2 = samplot.genome_interval('chr8', 300, 400)
ranges = [gi_1, gi_2]
i = samplot.genome_interval('chr8', 110, 120)
s, e = samplot.get_interval_range_plan_start_end(ranges, i)
self.assertEqual('chr8',s.chrm)
self.assertEqual(110,s.start)
self.assertEqual(110,s.end)
self.assertEqual('chr8',e.chrm)
self.assertEqual(120,e.start)
self.assertEqual(120,e.end)
i = samplot.genome_interval('chr8', 110, 220)
s, e = samplot.get_interval_range_plan_start_end(ranges, i)
self.assertEqual('chr8',s.chrm)
self.assertEqual(110,s.start)
self.assertEqual(110,s.end)
self.assertEqual('chr8',e.chrm)
self.assertEqual(200,e.start)
self.assertEqual(200,e.end)
i = samplot.genome_interval('chr8', 220, 320)
s, e = samplot.get_interval_range_plan_start_end(ranges, i)
self.assertEqual('chr8',s.chrm)
self.assertEqual(300,s.start)
self.assertEqual(300,s.end)
self.assertEqual('chr8',e.chrm)
self.assertEqual(320,e.start)
self.assertEqual(320,e.end)
i = samplot.genome_interval('chr8', 120, 320)
s, e = samplot.get_interval_range_plan_start_end(ranges, i)
self.assertEqual('chr8',s.chrm)
self.assertEqual(120,s.start)
self.assertEqual(120,s.end)
self.assertEqual('chr8',e.chrm)
self.assertEqual(320,e.start)
self.assertEqual(320,e.end)
i = samplot.genome_interval('chr8', 320, 520)
s, e = samplot.get_interval_range_plan_start_end(ranges, i)
self.assertEqual('chr8',s.chrm)
self.assertEqual(320,s.start)
self.assertEqual(320,s.end)
self.assertEqual('chr8',e.chrm)
self.assertEqual(400,e.start)
self.assertEqual(400,e.end)
i = samplot.genome_interval('chr8', 30, 50)
s, e = samplot.get_interval_range_plan_start_end(ranges, i)
self.assertEqual(None, s)
self.assertEqual(None, e)
i = samplot.genome_interval('chr8', 3000, 5000)
s, e = samplot.get_interval_range_plan_start_end(ranges, i)
self.assertEqual(None, s)
self.assertEqual(None, e)
#}}}
#}}}
#{{{class Test_splits(unittest.TestCase):
class Test_splits(unittest.TestCase):
#{{{def test_get_split_plan(self):
def test_get_split_plan(self):
splits = {}
hp = 0
splits[hp] = {}
read_name_1 = 'Test1'
ranges = [samplot.genome_interval('chr8', 100, 200),
samplot.genome_interval('chr8', 600, 800) ]
#both in same ragne
#Deletion
splits[hp][read_name_1] = [\
samplot.SplitRead('chr8', 100, 150, True, 0, False, False),
samplot.SplitRead('chr8', 170, 180, True, 50, False, False)]
plan = samplot.get_split_plan(ranges, splits[hp][read_name_1])
max_gap, steps = plan
self.assertEqual(20, max_gap)
self.assertEqual(1, len(steps))
self.assertEqual('SPLITREAD', steps[0].event)
self.assertEqual('Deletion', steps[0].info['TYPE'])
self.assertEqual('chr8', steps[0].start_pos.chrm)
self.assertEqual(150, steps[0].start_pos.start)
self.assertEqual(150, steps[0].start_pos.end)
self.assertEqual('chr8', steps[0].end_pos.chrm)
self.assertEqual(170, steps[0].end_pos.start)
self.assertEqual(170, steps[0].end_pos.end)
#Duplication
splits[hp][read_name_1] = [\
samplot.SplitRead('chr8', 100, 150, True, 0, False, False),
samplot.SplitRead('chr8', 130, 180, True, 50, False, False)]
plan = samplot.get_split_plan(ranges, splits[hp][read_name_1])
max_gap, steps = plan
self.assertEqual(20, max_gap)
self.assertEqual(1, len(steps))
self.assertEqual('SPLITREAD', steps[0].event)
self.assertEqual('Duplication', steps[0].info['TYPE'])
self.assertEqual('chr8', steps[0].start_pos.chrm)
self.assertEqual(150, steps[0].start_pos.start)
self.assertEqual(150, steps[0].start_pos.end)
self.assertEqual('chr8', steps[0].end_pos.chrm)
self.assertEqual(130, steps[0].end_pos.start)
self.assertEqual(130, steps[0].end_pos.end)
#Inversion
splits[hp][read_name_1] = [\
samplot.SplitRead('chr8', 100, 150, True, 0, False, False),
samplot.SplitRead('chr8', 151, 180, False, 50, False, False)]
plan = samplot.get_split_plan(ranges, splits[hp][read_name_1])
max_gap, steps = plan
self.assertEqual(30, max_gap)
self.assertEqual(1, len(steps))
self.assertEqual('SPLITREAD', steps[0].event)
self.assertEqual('Inversion', steps[0].info['TYPE'])
self.assertEqual('chr8', steps[0].start_pos.chrm)
self.assertEqual(150, steps[0].start_pos.start)
self.assertEqual(150, steps[0].start_pos.end)
self.assertEqual('chr8', steps[0].end_pos.chrm)
self.assertEqual(151, steps[0].end_pos.start)
self.assertEqual(151, steps[0].end_pos.end)
#both in same ragne
splits[hp][read_name_1] = [\
samplot.SplitRead('chr8', 100, 150, True, 0, False, False)]
plan = samplot.get_split_plan(ranges, splits[hp][read_name_1])
self.assertEqual(None, plan)
#both in same ragne
splits[hp][read_name_1] = [\
samplot.SplitRead('chr8', 550, 650, True, 0, False, False),
samplot.SplitRead('chr8', 700, 750, True, 50, False, False)]
plan = samplot.get_split_plan(ranges, splits[hp][read_name_1])
max_gap, steps = plan
self.assertEqual(50, max_gap)
self.assertEqual(1, len(steps))
self.assertEqual('SPLITREAD', steps[0].event)
self.assertEqual('Deletion', steps[0].info['TYPE'])
self.assertEqual('chr8', steps[0].start_pos.chrm)
self.assertEqual(650, steps[0].start_pos.start)
self.assertEqual(650, steps[0].start_pos.end)
self.assertEqual('chr8', steps[0].end_pos.chrm)
self.assertEqual(700, steps[0].end_pos.start)
self.assertEqual(700, steps[0].end_pos.end)
#both in same ragne
splits[hp][read_name_1] = [\
samplot.SplitRead('chr8', 150, 175, True, 0, False, False),
samplot.SplitRead('chr8', 650, 675, True, 50, False, False)]
plan = samplot.get_split_plan(ranges, splits[hp][read_name_1])
max_gap, steps = plan
self.assertEqual(475, max_gap)
self.assertEqual(1, len(steps))
self.assertEqual('SPLITREAD', steps[0].event)
self.assertEqual('Deletion', steps[0].info['TYPE'])
self.assertEqual('chr8', steps[0].start_pos.chrm)
self.assertEqual(175, steps[0].start_pos.start)
self.assertEqual(175, steps[0].start_pos.end)
self.assertEqual('chr8', steps[0].end_pos.chrm)
self.assertEqual(650, steps[0].end_pos.start)
self.assertEqual(650, steps[0].end_pos.end)
#inter chrom
ranges = [samplot.genome_interval('chr8', 100, 200),
samplot.genome_interval('chr9', 600, 800) ]
splits[hp][read_name_1] = [\
samplot.SplitRead('chr8', 150, 175, True, 0, False, False),
samplot.SplitRead('chr9', 650, 675, True, 50, False, False)]
plan = samplot.get_split_plan(ranges, splits[hp][read_name_1])
max_gap, steps = plan
self.assertEqual(samplot.INTERCHROM_YAXIS, max_gap)
self.assertEqual(1, len(steps))
self.assertEqual('SPLITREAD', steps[0].event)
self.assertEqual('InterChrm', steps[0].info['TYPE'])
self.assertEqual('chr8', steps[0].start_pos.chrm)
self.assertEqual(175, steps[0].start_pos.start)
self.assertEqual(175, steps[0].start_pos.end)
self.assertEqual('chr9', steps[0].end_pos.chrm)
self.assertEqual(650, steps[0].end_pos.start)
self.assertEqual(650, steps[0].end_pos.end)
splits[hp][read_name_1] = [\
samplot.SplitRead('chr8', 150, 175, True, 0, False, False),
samplot.SplitRead('chr9', 650, 675, False, 50, False, False)]
plan = samplot.get_split_plan(ranges, splits[hp][read_name_1])
max_gap, steps = plan
self.assertEqual(samplot.INTERCHROM_YAXIS, max_gap)
self.assertEqual(1, len(steps))
self.assertEqual('SPLITREAD', steps[0].event)
self.assertEqual('InterChrmInversion', steps[0].info['TYPE'])
self.assertEqual('chr8', steps[0].start_pos.chrm)
self.assertEqual(175, steps[0].start_pos.start)
self.assertEqual(175, steps[0].start_pos.end)
self.assertEqual('chr9', steps[0].end_pos.chrm)
self.assertEqual(650, steps[0].end_pos.start)
self.assertEqual(650, steps[0].end_pos.end)
#}}}
#{{{def test_get_splits_plan(self):
def test_get_splits_plan(self):
splits = {}
hp = 0
splits[hp] = {}
ranges = [samplot.genome_interval('chr8', 100, 200),
samplot.genome_interval('chr9', 600, 800) ]
#Deletion
splits[hp]['del'] = [\
samplot.SplitRead('chr8', 100, 150, True, 0, False, False),
samplot.SplitRead('chr8', 170, 180, True, 50, False, False)]
#Duplication
splits[hp]['dup'] = [\
samplot.SplitRead('chr8', 100, 150, True, 0, False, False),
samplot.SplitRead('chr8', 130, 180, True, 50, False, False)]
#Inversion
splits[hp]['inv'] = [\
samplot.SplitRead('chr8', 100, 150, True, 0, False, False),
samplot.SplitRead('chr8', 151, 180, False, 50, False, False)]
#Bad split
splits[hp]['bad'] = [\
samplot.SplitRead('chr8', 100, 150, True, 0, False, False)]
#Interchm
splits[hp]['interchm'] = [\
samplot.SplitRead('chr8', 150, 175, True, 0, False, False),
samplot.SplitRead('chr9', 650, 675, True, 50, False, False)]
#InterchmInv
splits[hp]['interchminv'] = [\
samplot.SplitRead('chr8', 150, 175, True, 0, False, False),
samplot.SplitRead('chr9', 650, 675, False, 50, False, False)]
plan = samplot.get_splits_plan(ranges, splits[hp])
max_gap, steps = plan
self.assertEqual(samplot.INTERCHROM_YAXIS, max_gap)
self.assertEqual(5, len(steps))
#}}}
#{{{def test_get_split_insert_size(self):
def test_get_split_insert_size(self):
splits = {}
hp = 0
splits[hp] = {}
read_name_1 = 'Test1'
#both in same ragne
splits[hp][read_name_1] = [\
samplot.SplitRead('chr8', 100, 150, True, 0, False, False),
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