tab to csv

# Read a tab delimited file (as saved by Excel) and output to a comma delimited file

# atf, gal, gpr files are tab delimited (GenePix files)

# The ‘Alternate method’ using the fileinput module converts the file in place.

import os, fileinput

def tab_to_csv(tab_name, csv_name):

try:

f1 = open(tab_name, 'r')

f2 = open(csv_name, 'w')

outList = []

for line in f1:

outList.append(','.join(line.rstrip('\t\n').split('\t'))+'\n')

f1.close()

f2.writelines(outList)

f2.close()

return True

except:

return False

import re

def readBlockData(fn):

dd = {}

fList = open(fn).readlines()

for line in fList:

line = line.strip('"\n\t')

if re.match('Block\d', line):

# tem = re.split('=', line)

tem = line.split('=')

dd[tem[0]] = [int(i) for i in tem[1].strip().split(', ')]

return dd

if __name__ == '__main__':

def run_script():

gpr_file = (os.path.join('H:\\', 'TEMP', 'temsys', 'GPR3.gpr'))

csv_file = (os.path.join('H:\\', 'TEMP', 'temsys', 'GPR5.txt'))

if tab_to_csv(gpr_file, csv_file):

print 'Tab delimited file conversion to comma delimited file was successful'

else:

print 'There was an error'

run_script()

dd = readBlockData(os.path.join('H:\\', 'TEMP', 'temsys', 'GPR3.gpr'))

for key in dd:

print '%s = %s' % (key, dd[key])

'''

Block4 = [4896, 4896, 100, 24, 175, 5, 175]

Block3 = [400, 4896, 100, 24, 175, 5, 175]

Block2 = [4896, 400, 100, 24, 175, 5, 175]

Block1 = [400, 400, 100, 24, 175, 5, 175]

'''

# Alternate method

gpr_file = (os.path.join('H:\\', 'TEMP', 'temsys', 'Copy of GPR3.gpr'))

import fileinput

for line in fileinput.input(gpr_file, True, '.bak'):

print ','.join(line.rstrip('\t\n').split('\t'))

# Before processing

"""

ATF 1

8 5

Type=GenePix ArrayList V1.0

BlockCount=4

BlockType=0

URL=http://genome-www.stanford.edu/cgi-bin/dbrun/SacchDB?find+Locus+%22[ID]%22

"Block1= 400, 400, 100, 24, 175, 5, 175"

"Block2= 4896, 400, 100, 24, 175, 5, 175"

"Block3= 400, 4896, 100, 24, 175, 5, 175"

"Block4= 4896, 4896, 100, 24, 175, 5, 175"

Block Column Row Name ID

1 1 1 VPS8 YAL002W

1 2 1 NTG1 YAL015C

"""

# After processing

"""

ATF,1

8,5