You can easily do this in bash instead of python. Suppose that you have your fastq files in one single folder, you can do something like:

for i in $(ls *.fastq.gz | uniq);
do
bowtie input=${i} output=${i}.out &&
tophat input=${i}.out output=${i}.tophat.out
done;

Of course, that's just a small suggestion... Just write the proper code for your needs.

Hope it helps!