$ cat file
This
is,
are,
a,
a longer,  harder,  faster line
$ python3 -c "[print( (',').join([s for s in l.split(',') if not s == ''])+',') for l in open('file').read().splitlines()]"
This,
is, ,
are, ,
a, ,
a longer,  harder,  faster line,

This,
is,
are,
a,
a longer,  harder,  faster line,

$ python --version
Python 3.5.2

Python 3.5.1+

$ od -c file
0000000   T   h   i   s  \n   i   s   ,      \n   a   r   e   ,      \n
0000020   a   ,      \n   a       l   o   n   g   e   r   ,           h
0000040   a   r   d   e   r   ,           f   a   s   t   e   r       l
0000060   i   n   e  \n

print(*[line.rstrip(",\n") for line in open("fileee")], sep=",\n", end=",\n")

bytecommander@BC-AlkaliMetal:~$ cat fileee
This
is,
are, were,,,,
a,
a longer,  harder,  faster line
bytecommander@BC-AlkaliMetal:~$ python3 -c 'print(*[line.rstrip(",\n") for line in open("fileee")], sep=",\n", end=",\n")'
This,
is,
are, were,
a,
a longer,  harder,  faster line,

    $ ls -lh newfile
    -rw-r--r-- 1 terdon terdon 14M Jul 13 17:49 newfile
    $ time python3 -c "[print( (',').join([s for s in l.split(',') if not s == ''])+',') for l in open('newfile').read().splitlines()]" > /dev/null

    real	0m0.310s
    user	0m0.293s
    sys	0m0.013s
$ time perl -lne 'printf join ",", (grep {$_ ne ""}split(/,/) ); print ","' newfile > /dev/null

real	0m0.171s
user	0m0.170s
sys	0m0.000s
$ time python3 -c "[print( (',').join([s for s in l.split(',') if not s == ''])+',') for l in open('newfile').read().splitlines()]" > /dev/null

wget heanet.dl.sourceforge.net/project/warzone2100\
warzone2100/Videos/high-quality-en/sequences.wz

s =  "monkey,,,,,,,!!!\n"
print(s.strip("\n,!"))

> monkey

@edwinksl ┌─[00:36:01]─[michael@NEXUS-ONE]
└──> euler $ uname -a
Linux NEXUS-ONE 4.4.0-31-generic #50-Ubuntu SMP Wed Jul 13 00:07:12 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux