Python bcftbx.TabFile类代码示例

 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_transpose_tab_file(self):
     """Test transposing TabFile
     """
     tabfile1 = TabFile('test',self.fp,first_line_is_header=False)
     tabfile2 = tabfile1.transpose()
     self.assertEqual(len(tabfile1),tabfile2.nColumns())
     self.assertEqual(len(tabfile2),tabfile1.nColumns())

 def test_write_data(self):
     """Write data to file-like object
     """
     tabfile = TabFile('test',self.fp)
     fp = cStringIO.StringIO()
     tabfile.write(fp=fp)
     self.assertEqual(fp.getvalue(),self.data)
     fp.close()

 def test_reverse_sort_on_column(self):
     """Sort data on a numerical column into (reverse) descending order
     """
     tabfile = TabFile('test',self.fp,first_line_is_header=True)
     tabfile.sort(lambda line: line['data'],reverse=True)
     sorted_data = [6.8,5.7,3.4]
     for i in range(len(tabfile)):
         self.assertEqual(tabfile[i]['data'],sorted_data[i])

 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_write_data_with_header(self):
     """Write data to file-like object including a header line
     """
     tabfile = TabFile('test',self.fp,first_line_is_header=True,delimiter=',')
     fp = cStringIO.StringIO()
     tabfile.write(fp=fp,include_header=True)
     self.assertEqual(fp.getvalue(),self.header.replace('\t',',')+self.data.replace('\t',','))
     fp.close()

 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_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_load_data_with_header(self):
     """Create and load Tabfile using first line as header
     """
     tabfile = TabFile('test',self.fp,first_line_is_header=True)
     self.assertEqual(len(tabfile),3,"Input has 3 lines of data")
     self.assertEqual(tabfile.header(),['chr','start','end','data'],"Wrong header")
     self.assertEqual(str(tabfile[0]),"chr1\t1\t234\t4.6","Incorrect string representation")
     self.assertEqual(tabfile[2]['chr'],'chr2',"Incorrect data")
     self.assertEqual(tabfile.nColumns(),4)

 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_unexpected_uncommented_header(self):
     """Test reading in a tab file with an unexpected uncommented header
     """
     tabfile = TabFile('test',self.fp)
     self.assertEqual(len(tabfile),4,"Input has 4 lines of data")
     self.assertEqual(tabfile.header(),[],"Wrong header")
     self.assertEqual(str(tabfile[0]),"chr\tstart\tend\tdata","Incorrect string representation")
     self.assertRaises(KeyError,tabfile[3].__getitem__,'chr')
     self.assertEqual(tabfile.nColumns(),4)

 def test_expected_uncommented_header(self):
     """Test reading in a tab file with an expected uncommented header
     """
     tabfile = TabFile('test',self.fp,first_line_is_header=True)
     self.assertEqual(len(tabfile),3,"Input has 3 lines of data")
     self.assertEqual(tabfile.header(),['chr','start','end','data'],"Wrong header")
     self.assertEqual(str(tabfile[0]),"chr1\t1\t234\t4.6","Incorrect string representation")
     self.assertEqual(tabfile[2]['chr'],'chr2',"Incorrect data")
     self.assertEqual(tabfile.nColumns(),4)

 def test_load_data(self):
     """Create and load new TabFile instance
     """
     tabfile = TabFile('test',self.fp,delimiter=',')
     self.assertEqual(len(tabfile),3,"Input has 3 lines of data")
     self.assertEqual(tabfile.header(),[],"Header should be empty")
     self.assertEqual(str(tabfile[0]),"chr1,1,234,4.6","Incorrect string representation")
     self.assertEqual(tabfile[2][0],'chr2',"Incorrect data")
     self.assertEqual(tabfile.nColumns(),4)
     self.assertEqual(tabfile.filename(),'test')

 def test_insert_line_with_tab_data(self):
     """Insert line into a TabFile populated from tabbed data
     """
     data = 'chr1\t10000\t20000\t+'
     tabfile = TabFile('test',self.fp)
     self.assertEqual(len(tabfile),3)
     line = tabfile.insert(2,tabdata=data)
     self.assertEqual(len(tabfile),4)
     # Check new line is correct
     self.assertTrue(str(line) == data)