def test_append_line(self):
"""Append a line to a file
"""
tabfile = TabFile('test',self.fp,first_line_is_header=True,delimiter=',')
line = 'chr3,10,9,8'
tabfile.append(tabdata=line)
self.assertEqual(str(tabfile[-1]),line)
def test_append_line_as_data(self):
"""Append a line to a file with data supplied as a list
"""
tabfile = TabFile('test',self.fp,first_line_is_header=True,delimiter=',')
data = ['chr3','10','9','8']
tabfile.append(data=data)
self.assertEqual(str(tabfile[-1]),','.join([str(x) for x in data]))
def test_add_tab_data_to_new_tabfile(self):
"""Test adding data as a tab-delimited line to a new empty TabFile
"""
data = 'chr1\t10000\t20000\t+'
tabfile = TabFile()
tabfile.append(tabdata=data)
self.assertEqual(len(tabfile),1,"TabFile should now have one line")
self.assertEqual(str(tabfile[0]),data)
def test_add_tab_data_to_new_tabfile(self):
"""Test adding data as a tab-delimited line to a new empty TabFile
"""
data = 'chr1\t10000\t20000\t+'
tabfile = TabFile()
tabfile.append(tabdata=data)
self.assertEqual(len(tabfile), 1, "TabFile should now have one line")
self.assertEqual(str(tabfile[0]), data)
def test_convert_values_to_type_append_tabdata(self):
"""Convert input values to appropriate types (e.g. integer) when appending tabdata
"""
tabfile = TabFile('test', self.fp, first_line_is_header=True)
tabfile.append(tabdata="chr3\t5678\t7.9")
for line in tabfile:
self.assertTrue(isinstance(line[0], str))
self.assertTrue(isinstance(line[1], (int, long)))
self.assertTrue(isinstance(line[2], float))
def test_convert_values_to_type_append_tabdata(self):
"""Convert input values to appropriate types (e.g. integer) when appending tabdata
"""
tabfile = TabFile('test',self.fp,first_line_is_header=True)
tabfile.append(tabdata="chr3\t5678\t7.9")
for line in tabfile:
self.assertTrue(isinstance(line[0],str))
self.assertTrue(isinstance(line[1],(int,long)))
self.assertTrue(isinstance(line[2],float))
def test_add_data_to_new_tabfile(self):
"""Test adding data as a list of items to a new empty TabFile
"""
data = ['chr1',10000,20000,'+']
tabfile = TabFile()
tabfile.append(data=data)
self.assertEqual(len(tabfile),1,"TabFile should now have one line")
for i in range(len(data)):
self.assertEqual(tabfile[0][i],data[i])
def test_add_data_to_new_tabfile(self):
"""Test adding data as a list of items to a new empty TabFile
"""
data = ['chr1', 10000, 20000, '+']
tabfile = TabFile()
tabfile.append(data=data)
self.assertEqual(len(tabfile), 1, "TabFile should now have one line")
for i in range(len(data)):
self.assertEqual(tabfile[0][i], data[i])
def test_convert_values_to_str_append_tabdata(self):
"""Convert all input values to strings when appending tabdata
"""
tabfile = TabFile('test',self.fp,first_line_is_header=True,
convert=False)
tabfile.append(tabdata="chr3\t5678\t7.9")
for line in tabfile:
for value in line:
self.assertTrue(isinstance(value,str))
def test_convert_values_to_str_append_list(self):
"""Convert all input values to strings when appending a list
"""
tabfile = TabFile('test',self.fp,first_line_is_header=True,
convert=False)
tabfile.append(data=["chr3","5678","7.9"])
tabfile.append(data=["chr3",5678,7.9])
for line in tabfile:
for value in line:
self.assertTrue(isinstance(value,str))
def test_convert_values_to_type_append_list(self):
"""Convert input values to appropriate types (e.g. integer) when appending a list
"""
tabfile = TabFile('test', self.fp, first_line_is_header=True)
tabfile.append(data=["chr3", "5678", "7.9"])
tabfile.append(data=["chr3", 5678, 7.9])
for line in tabfile:
self.assertTrue(isinstance(line[0], str))
self.assertTrue(isinstance(line[1], (int, long)))
self.assertTrue(isinstance(line[2], float))
def test_append_line_as_data(self):
"""Append a line to a file with data supplied as a list
"""
tabfile = TabFile('test',
self.fp,
first_line_is_header=True,
delimiter=',')
data = ['chr3', '10', '9', '8']
tabfile.append(data=data)
self.assertEqual(str(tabfile[-1]), ','.join([str(x) for x in data]))
def test_append_line(self):
"""Append a line to a file
"""
tabfile = TabFile('test',
self.fp,
first_line_is_header=True,
delimiter=',')
line = 'chr3,10,9,8'
tabfile.append(tabdata=line)
self.assertEqual(str(tabfile[-1]), line)
def test_convert_values_to_type_append_list(self):
"""Convert input values to appropriate types (e.g. integer) when appending a list
"""
tabfile = TabFile('test',self.fp,first_line_is_header=True)
tabfile.append(data=["chr3","5678","7.9"])
tabfile.append(data=["chr3",5678,7.9])
for line in tabfile:
self.assertTrue(isinstance(line[0],str))
self.assertTrue(isinstance(line[1],(int,long)))
self.assertTrue(isinstance(line[2],float))
def test_convert_values_to_str_append_tabdata(self):
"""Convert all input values to strings when appending tabdata
"""
tabfile = TabFile('test',
self.fp,
first_line_is_header=True,
convert=False)
tabfile.append(tabdata="chr3\t5678\t7.9")
for line in tabfile:
for value in line:
self.assertTrue(isinstance(value, str))
def test_convert_values_to_str_append_list(self):
"""Convert all input values to strings when appending a list
"""
tabfile = TabFile('test',
self.fp,
first_line_is_header=True,
convert=False)
tabfile.append(data=["chr3", "5678", "7.9"])
tabfile.append(data=["chr3", 5678, 7.9])
for line in tabfile:
for value in line:
self.assertTrue(isinstance(value, str))
def test_append_tab_data_line(self):
"""Append a TabDataLine to a TabFile
"""
tabfile = TabFile('test',self.fp)
self.assertEqual(len(tabfile),3)
tabdataline = TabDataLine('chr1\t10000\t20000\t+')
line = tabfile.append(tabdataline=tabdataline)
self.assertEqual(len(tabfile),4)
# Check new line is correct
self.assertTrue(line is tabdataline)
def test_append_line_with_tab_data(self):
"""Append line to a TabFile populated from tabbed data
"""
data = 'chr1\t10000\t20000\t+'
tabfile = TabFile('test',self.fp)
self.assertEqual(len(tabfile),3)
line = tabfile.append(tabdata=data)
self.assertEqual(len(tabfile),4)
# Check new line is correct
self.assertTrue(str(line) == data)
def test_append_tab_data_line(self):
"""Append a TabDataLine to a TabFile
"""
tabfile = TabFile('test', self.fp)
self.assertEqual(len(tabfile), 3)
tabdataline = TabDataLine('chr1\t10000\t20000\t+')
line = tabfile.append(tabdataline=tabdataline)
self.assertEqual(len(tabfile), 4)
# Check new line is correct
self.assertTrue(line is tabdataline)
def test_append_empty_line(self):
"""Append a blank line to a TabFile
"""
tabfile = TabFile('test', self.fp)
self.assertEqual(len(tabfile), 3)
line = tabfile.append()
self.assertEqual(len(tabfile), 4)
# Check new line is empty
for i in range(len(line)):
self.assertTrue(str(line[i]) == '')
def test_append_empty_line(self):
"""Append a blank line to a TabFile
"""
tabfile = TabFile('test',self.fp)
self.assertEqual(len(tabfile),3)
line = tabfile.append()
self.assertEqual(len(tabfile),4)
# Check new line is empty
for i in range(len(line)):
self.assertTrue(str(line[i]) == '')
def test_append_line_with_tab_data(self):
"""Append line to a TabFile populated from tabbed data
"""
data = 'chr1\t10000\t20000\t+'
tabfile = TabFile('test', self.fp)
self.assertEqual(len(tabfile), 3)
line = tabfile.append(tabdata=data)
self.assertEqual(len(tabfile), 4)
# Check new line is correct
self.assertTrue(str(line) == data)
def test_append_line_with_data(self):
"""Append line to a TabFile populated with data
"""
data = ['chr1', 678, 901, 6.1]
tabfile = TabFile('test', self.fp)
self.assertEqual(len(tabfile), 3)
line = tabfile.append(data=data)
self.assertEqual(len(tabfile), 4)
# Check new line is correct
for i in range(len(data)):
self.assertTrue(line[i] == data[i])
def test_append_line_with_data(self):
"""Append line to a TabFile populated with data
"""
data = ['chr1',678,901,6.1]
tabfile = TabFile('test',self.fp)
self.assertEqual(len(tabfile),3)
line = tabfile.append(data=data)
self.assertEqual(len(tabfile),4)
# Check new line is correct
for i in range(len(data)):
self.assertTrue(line[i] == data[i])