class tXmapFile(tFile_base):
def setUp(self):
with open(self.input_file, "w"):
self.obj=XmapFile(self.input_file)
def test_getExtension(self):
self.assertEquals("xmap", XmapFile.getExtension())
def test_parse(self):
expected=XmapFile_iter(self.input_file)
self.assertEqual(expected, self.obj.parse())
def test_write(self):
expected="1 2 3 1.0 2.0 1.0 2.0 + 999.9 1DM 1.0 1.0 1 (1,1)(1,2)\n"
alignment=Mock(alignment_id=1, query_id=2, anchor_id=3, query_start=1.0, query_end=2.0, anchor_start=1.0, anchor_end=2.0, orientation="+", confidence=999.9, hit_enum="1DM", query_len=1.0, anchor_len=1.0, label_channel="1", alignment="(1,1)(1,2)")
with open("test_file", "w") as o_file:
self.obj.write(alignment, o_file)
with open("test_file") as i_file:
actual=i_file.readline()
os.remove("test_file")
self.assertEqual(expected, actual)
class tFindBreakpoints(tScripts):
maxDiff=None
xmap_name='file.xmap'
xmap_writer=None
xmap=None
query_cmap_name='file_r.cmap'
query_cmap=None
anchor_cmap_name='file_q.cmap'
anchor_cmap=None
cmap_writer=None
def setUp(self):
self.xmap=open(self.xmap_name, 'w')
self.xmap_writer=XmapFile(self.xmap_name)
self.query_cmap=open(self.query_cmap_name, 'w')
self.anchor_cmap=open(self.anchor_cmap_name, 'w')
self.cmap_writer=CmapFile(self.query_cmap_name)
def tearDown(self):
self.xmap.close()
self.query_cmap.close()
self.anchor_cmap.close()
os.remove(self.xmap_name)
os.remove(self.query_cmap_name)
os.remove(self.anchor_cmap_name)
### Bad input ###
def test_badInput_none(self):
expected_stdout="usage: find_breakpoints.py [-h] xmap_file\nfind_breakpoints.py: error: too few arguments\n"
expected_returnCode=2
expecteds=[expected_stdout, expected_returnCode]
actual_stdout=None
try:
actual_stdout=subprocess.check_output("../scripts/find_breakpoints.py", stderr=subprocess.STDOUT)
actual_returnCode=0
except subprocess.CalledProcessError as error:
actual_stdout=error.output
actual_returnCode=error.returncode
except:
raise
actuals=[actual_stdout, actual_returnCode]
self.assertEquals(expecteds, actuals)
def test_badInput_notAFile(self):
expected_stdout="The .xmap alignment file you specified, file.xmap.bed.ext, could not be found\n"
expected_returnCode=1
expecteds=[expected_stdout, expected_returnCode]
actual_stdout=None
try:
actual_stdout=subprocess.check_output(["../scripts/find_breakpoints.py",self.xmap_name+".bed.ext"], stderr=subprocess.STDOUT)
actual_returnCode=0
except subprocess.CalledProcessError as error:
actual_stdout=error.output
actual_returnCode=error.returncode
except:
raise
actuals=[actual_stdout, actual_returnCode]
self.assertEquals(expecteds, actuals)
@unittest.skip('not_implemented')
def test_badInput_notXmap(self):
pass
def test_badInput_contigInXmapNotInAnchorCmap(self):
for label_position in xrange(1,1000):
label=Mock(contig_id=1, contig_len=1000, contig_site_count=1000, label_id=label_position, channel="1", position=label_position, stdev=0, coverage=1, occurrences=1)
self.cmap_writer.write(label, self.query_cmap)
self.query_cmap.close()
alignment=Mock(alignment_id=1, query_id=1, anchor_id=1, query_start=2, query_end=998, anchor_start=1, anchor_end=1000, orientation='+', confidence=250,hit_enum="*", query_len=1000, anchor_len=1000, label_channel="1", alignment="*")
self.xmap_writer.write(alignment, self.xmap)
self.xmap.close()
expected_stdout="The .xmap alignment ("+self.xmap_name+") file contains a contig id (1) that was not found in one of the .cmap contig files ("+self.anchor_cmap_name+")\n"
expected_returnCode=1
expecteds=[expected_stdout, expected_returnCode]
try:
actual_stdout=subprocess.check_output(["../scripts/find_breakpoints.py",self.xmap_name], stderr=subprocess.STDOUT)
actual_returnCode=0
except subprocess.CalledProcessError as error:
actual_stdout=error.output
actual_returnCode=error.returncode
except:
raise
actuals=[actual_stdout, actual_returnCode]
self.assertEquals(expecteds, actuals)
def test_badInput_contigInXmapNotInQueryCmap(self):
for label_position in xrange(1,1000):
label=Mock(contig_id=1, contig_len=1000, contig_site_count=1000, label_id=label_position, channel="1", position=label_position, stdev=0, coverage=1, occurrences=1)
self.cmap_writer.write(label, self.anchor_cmap)
self.anchor_cmap.close()
alignment=Mock(alignment_id=1, query_id=1, anchor_id=1, query_start=2, query_end=998, anchor_start=1, anchor_end=1000, orientation='+', confidence=250,hit_enum="*", query_len=1000, anchor_len=1000, label_channel="1", alignment="*")
self.xmap_writer.write(alignment, self.xmap)
self.xmap.close()
expected_stdout="The .xmap alignment ("+self.xmap_name+") file contains a contig id (1) that was not found in one of the .cmap contig files ("+self.query_cmap_name+")\n"
expected_returnCode=1
expecteds=[expected_stdout, expected_returnCode]
try:
actual_stdout=subprocess.check_output(["../scripts/find_breakpoints.py",self.xmap_name], stderr=subprocess.STDOUT)
actual_returnCode=0
except subprocess.CalledProcessError as error:
actual_stdout=error.output
actual_returnCode=error.returncode
except:
raise
actuals=[actual_stdout, actual_returnCode]
self.assertEquals(expecteds, actuals)
def test_badInput_cantFindCmap(self):
os.remove(self.query_cmap_name)
os.remove(self.anchor_cmap_name)
expected_stdout="Some of the .cmap contig files associated with your .xmap alignment file could not be found. More specifically, Unable to find query, anchor maps.\n"
expected_returnCode=1
expecteds=[expected_stdout, expected_returnCode]
actual_stdout=None
try:
actual_stdout=subprocess.check_output(["../scripts/find_breakpoints.py",self.xmap_name], stderr=subprocess.STDOUT)
actual_returnCode=0
except subprocess.CalledProcessError as error:
actual_stdout=error.output
actual_returnCode=error.returncode
except:
raise
actuals=[actual_stdout, actual_returnCode]
with open(self.query_cmap_name, 'w'):
pass
with open(self.anchor_cmap_name, 'w'):
pass
self.assertEquals(expecteds, actuals)
### One alignment only ###
def test_oneAlignment_no5PercentOverhang(self):
for label_position in xrange(1,1000):
label=Mock(contig_id=1, contig_len=1000, contig_site_count=1000, label_id=label_position, channel="1", position=label_position, stdev=0, coverage=1, occurrences=1)
self.cmap_writer.write(label, self.query_cmap)
self.cmap_writer.write(label, self.anchor_cmap)
self.query_cmap.close()
self.anchor_cmap.close()
alignment=Mock(alignment_id=1, query_id=1, anchor_id=1, query_start=2, query_end=998, anchor_start=1, anchor_end=1000, orientation='+', confidence=250,hit_enum="*", query_len=1000, anchor_len=1000, label_channel="1", alignment="*")
self.xmap_writer.write(alignment, self.xmap)
self.xmap.close()
expected_stdout=""
expected_returnCode=0
expecteds=[expected_stdout, expected_returnCode]
try:
actual_stdout=subprocess.check_output(["../scripts/find_breakpoints.py",self.xmap_name], stderr=subprocess.STDOUT)
actual_returnCode=0
except subprocess.CalledProcessError as error:
actual_stdout=error.output
actual_returnCode=error.returncode
except:
raise
actuals=[actual_stdout, actual_returnCode]
self.assertEquals(expecteds, actuals)
def test_oneAlignment_noLabeledOverhang(self):
for label_position in xrange(1,500):
label=Mock(contig_id=1, contig_len=1000, contig_site_count=1000, label_id=label_position, channel="1", position=label_position, stdev=0, coverage=1, occurrences=1)
self.cmap_writer.write(label, self.query_cmap)
self.cmap_writer.write(label, self.anchor_cmap)
self.query_cmap.close()
self.anchor_cmap.close()
alignment=Mock(alignment_id=1, query_id=1, anchor_id=1, query_start=2, query_end=500, anchor_start=1, anchor_end=500, orientation='+', confidence=250,hit_enum="*", query_len=1000, anchor_len=1000, label_channel="1", alignment="*")
self.xmap_writer.write(alignment, self.xmap)
self.xmap.close()
expected_stdout=""
expected_returnCode=0
expecteds=[expected_stdout, expected_returnCode]
try:
actual_stdout=subprocess.check_output(["../scripts/find_breakpoints.py",self.xmap_name], stderr=subprocess.STDOUT)
actual_returnCode=0
except subprocess.CalledProcessError as error:
actual_stdout=error.output
actual_returnCode=error.returncode
except:
raise
actuals=[actual_stdout, actual_returnCode]
self.assertEquals(expecteds, actuals)
def test_oneAlignment_oneSingleLabelOverhang(self):
for label_position in xrange(1,502):
label=Mock(contig_id=1, contig_len=1000, contig_site_count=1000, label_id=label_position, channel="1", position=label_position, stdev=0, coverage=1, occurrences=1)
self.cmap_writer.write(label, self.query_cmap)
self.cmap_writer.write(label, self.anchor_cmap)
self.query_cmap.close()
self.anchor_cmap.close()
alignment=Mock(alignment_id=1, query_id=1, anchor_id=1, query_start=2, query_end=500, anchor_start=1, anchor_end=500, orientation='+', confidence=250,hit_enum="*", query_len=1000, anchor_len=1000, label_channel="1", alignment="*")
self.xmap_writer.write(alignment, self.xmap)
self.xmap.close()
expected_stdout="Chr01\t500\t501\t1\t250.0\t+\n"
expected_returnCode=0
expecteds=[expected_stdout, expected_returnCode]
try:
actual_stdout=subprocess.check_output(["../scripts/find_breakpoints.py",self.xmap_name], stderr=subprocess.STDOUT)
actual_returnCode=0
except subprocess.CalledProcessError as error:
actual_stdout=error.output
actual_returnCode=error.returncode
except:
raise
actuals=[actual_stdout, actual_returnCode]
self.assertEquals(expecteds, actuals)
def test_oneAlignment_oneLabeledOverhang(self):
for label_position in xrange(1,1000):
label=Mock(contig_id=1, contig_len=1000, contig_site_count=1000, label_id=label_position, channel="1", position=label_position, stdev=0, coverage=1, occurrences=1)
self.cmap_writer.write(label, self.query_cmap)
self.cmap_writer.write(label, self.anchor_cmap)
self.query_cmap.close()
self.anchor_cmap.close()
alignment=Mock(alignment_id=1, query_id=1, anchor_id=1, query_start=2, query_end=500, anchor_start=1, anchor_end=500, orientation='+', confidence=250,hit_enum="*", query_len=1000, anchor_len=1000, label_channel="1", alignment="*")
self.xmap_writer.write(alignment, self.xmap)
self.xmap.close()
expected_stdout="Chr01\t500\t502\t1\t250.0\t+\n"
expected_returnCode=0
expecteds=[expected_stdout, expected_returnCode]
try:
actual_stdout=subprocess.check_output(["../scripts/find_breakpoints.py",self.xmap_name], stderr=subprocess.STDOUT)
actual_returnCode=0
except subprocess.CalledProcessError as error:
actual_stdout=error.output
actual_returnCode=error.returncode
except:
raise
actuals=[actual_stdout, actual_returnCode]
self.assertEquals(expecteds, actuals)
### Multiple alignments ###
@unittest.skip('not implmemented')
def test_multipleAligns_noTwoLabelOverhang(self):
pass
