def columnAddRowCounter(self, where_to_add_index, new_file_name,
is_first_row_title):
"""
This methods adds a new column that counts the number of rows.
Keyword arguments:
where_to_add_index: the index of the location that row count
is added
new_file_name: the name of a new file
is_first_row_title: 1 for not including
"""
data = ""
counter = 1
for line in self.data:
if (is_first_row_title == 1):
is_first_row_title = 0
continue
words = line.split()
words.insert(where_to_add_index, str(counter))
data = '\t'.join(words) + "\n"
ft = FileTask(new_file_name, 'a')
ft.writeFile(data)
counter += 1
def __init__(self, file_name, open_mode):
"""
Constructor
Keyword arguments:
file_name -- the input file
open_mode -- the file operation mode ('r', 'w' or 'a')
"""
self.ft = FileTask(file_name, open_mode)
self.ft.readFile()
self.data = self.ft.getData()
def columnsRangeRemove(self, column_start, column_end, new_file_name):
"""
"""
data = ""
for line in self.data:
words = line.split()
first_half = words[:column_start - 1]
second_half = words[column_end - 1:]
words = first_half + second_half
#print words
data = ' '.join(words) + "\n"
ft = FileTask(new_file_name, 'a')
ft.writeFile(data)
def columnAddFixChr(self, where_to_add_index, chr_index, new_file_name):
"""
This method is used for changing the chr column to the desired format.
Keyboard argumants:
where_to_add_index: the index of new field position
new_file_name: the name of new file
"""
data = ""
ft = FileTask(new_file_name, 'a')
for line in self.data:
words = line.split()
chr_val = words[chr_index]
chr_val = "chr" + chr_val
words.insert(where_to_add_index, chr_val)
data = ' '.join(words) + "\n"
ft.writeFile(data)
def columnAddBySum(self, column_number1, column_number2, new_file_name):
"""
This method sums up two given column and saves the result into a new column.
The new column is at the end.
Keyword arguments:
column_number1: the first column for adding
column_number2: the second column for adding
new_file_name: the name of a new file
"""
data = ""
for line in self.data:
words = line.split()
col1 = words[column_number1]
col2 = words[column_number2]
sum_col = int(col1) + int(col2)
words.append(str(sum_col))
data = data + ' '.join(words) + "\n"
ft = FileTask(new_file_name, 'w')
ft.writeFile(data)
def columnRemove(self, column_number, new_file_name):
"""
This method removes a specified column from a file.
Keyword arguments:
column_number: the index of column that is removed
new_file_name: the name of a new file
"""
data = ""
for line in self.data:
words = line.split()
if (column_number == 1):
words = words[1:]
else:
first_half = words[0:column_number]
second_half = words[column_number + 1:]
words = first_half + second_half
data = data + ' '.join(words) + "\n"
ft = FileTask(new_file_name, 'w')
ft.writeFile(data)
def columnAddBySubtract(self, column_number1, column_number2,
new_file_name, subtract_flag):
"""
This method subtract two given column and saves the result into a new column.
The new column is at the end.
Keyword arguments:
column_number1: the first column for adding
column_number2: the second column for adding
new_file_name: the name of a new file
subtract_flag: if its 1 then column1 - column2 and if its 2 otherwise
"""
data = ""
for line in self.data:
words = line.split()
col1 = words[column_number1]
col2 = words[column_number2]
try:
if subtract_flag == 1:
result_col = float(col1) - float(col2)
else:
result_col = float(col2) - float(col1)
except (ValueError):
print words
pass
words.append(str(result_col))
data = data + ' '.join(words) + "\n"
print words
ft = FileTask(new_file_name, 'w')
ft.writeFile(data)
class TextFileTools:
text_file_tools_count = 0
def __init__(self, file_name, open_mode):
"""
Constructor
Keyword arguments:
file_name -- the input file
open_mode -- the file operation mode ('r', 'w' or 'a')
"""
self.ft = FileTask(file_name, open_mode)
self.ft.readFile()
self.data = self.ft.getData()
def columnRemove(self, column_number, new_file_name):
"""
This method removes a specified column from a file.
Keyword arguments:
column_number: the index of column that is removed
new_file_name: the name of a new file
"""
data = ""
for line in self.data:
words = line.split()
if (column_number == 1):
words = words[1:]
else:
first_half = words[0:column_number]
second_half = words[column_number + 1:]
words = first_half + second_half
data = data + ' '.join(words) + "\n"
ft = FileTask(new_file_name, 'w')
ft.writeFile(data)
def columnsRangeRemove(self, column_start, column_end, new_file_name):
"""
"""
data = ""
for line in self.data:
words = line.split()
first_half = words[:column_start - 1]
second_half = words[column_end - 1:]
words = first_half + second_half
#print words
data = ' '.join(words) + "\n"
ft = FileTask(new_file_name, 'a')
ft.writeFile(data)
#ft = FileTask(new_file_name, 'w')
#ft.writeFile(data)
def columnAddBySum(self, column_number1, column_number2, new_file_name):
"""
This method sums up two given column and saves the result into a new column.
The new column is at the end.
Keyword arguments:
column_number1: the first column for adding
column_number2: the second column for adding
new_file_name: the name of a new file
"""
data = ""
for line in self.data:
words = line.split()
col1 = words[column_number1]
col2 = words[column_number2]
sum_col = int(col1) + int(col2)
words.append(str(sum_col))
data = data + ' '.join(words) + "\n"
ft = FileTask(new_file_name, 'w')
ft.writeFile(data)
def columnAddBySubtract(self, column_number1, column_number2,
new_file_name, subtract_flag):
"""
This method subtract two given column and saves the result into a new column.
The new column is at the end.
Keyword arguments:
column_number1: the first column for adding
column_number2: the second column for adding
new_file_name: the name of a new file
subtract_flag: if its 1 then column1 - column2 and if its 2 otherwise
"""
data = ""
for line in self.data:
words = line.split()
col1 = words[column_number1]
col2 = words[column_number2]
try:
if subtract_flag == 1:
result_col = float(col1) - float(col2)
else:
result_col = float(col2) - float(col1)
except (ValueError):
print words
pass
words.append(str(result_col))
data = data + ' '.join(words) + "\n"
print words
ft = FileTask(new_file_name, 'w')
ft.writeFile(data)
def columnAddRowCounter(self, where_to_add_index, new_file_name,
is_first_row_title):
"""
This methods adds a new column that counts the number of rows.
Keyword arguments:
where_to_add_index: the index of the location that row count
is added
new_file_name: the name of a new file
is_first_row_title: 1 for not including
"""
data = ""
counter = 1
for line in self.data:
if (is_first_row_title == 1):
is_first_row_title = 0
continue
words = line.split()
words.insert(where_to_add_index, str(counter))
data = '\t'.join(words) + "\n"
ft = FileTask(new_file_name, 'a')
ft.writeFile(data)
counter += 1
def columnAddFixChr(self, where_to_add_index, chr_index, new_file_name):
"""
This method is used for changing the chr column to the desired format.
Keyboard argumants:
where_to_add_index: the index of new field position
new_file_name: the name of new file
"""
data = ""
ft = FileTask(new_file_name, 'a')
for line in self.data:
words = line.split()
chr_val = words[chr_index]
chr_val = "chr" + chr_val
words.insert(where_to_add_index, chr_val)
data = ' '.join(words) + "\n"
ft.writeFile(data)
#ft = FileTask(new_file_name, 'w')
#ft.writeFile(data)
def mergeTextFiles(self, file_folder_path, merged_file_name,
add_line_count):
"""
pattern matching
"""
file_list = glob.glob(file_folder_path)
for file_item in file_list:
print file_item
# def writeNewFile(self, new_file_name):
"""
"""
# def columnAdd(self, Data):
"""