If you specifically want to do this in python a couple of approaches are below (note you don't have to use sys and argv or stdin for this, it just makes running them from the commandline easy).

The BioPython way (easy parsing)

You can simply re-parse it through:

import sys
from Bio import SeqIO

SeqIO.convert(sys.argv[1], 'fasta', sys.argv[2], 'fasta')

as a one liner (using the shell STDIN):

cat file.fasta | python -c "import sys; from Bio import SeqIO; SeqIO.convert(sys.stdin, sys.argv[1], sys.stdout, sys.argv[2]);" "$1" "$2"

The pure python way

import sys

with open(sys.argv[1], 'r') as fh:
    for line in fh:
        if not line.startswith("\n"):
            print(line, end = "")   # line.rstrip("\n") would also work

(Note, the above approach requires Python 3, or you will need to add a from __future__ import print_function)

Just use sed:

cat test.txt ;

fghfgh


fghhf


fh
f
gh
fgh
fgfh
fhfh
fh
hg










fghfgh
f
f

Now strip the empty lines:

sed '/^$/d' test.txt ;
fghfgh
fghhf
fh
f
gh
fgh
fgfh
fhfh
fh
hg
fghfgh
f
f

sed -i to replace the file as is (risky).

Kevin