Why is python no longer waiting for os.system to finish?

Question

I have the following function, which has been working great for months. I have not updated my version of Python (unless it happens behind the scenes?).

def Blast(type, protein_sequence, start, end, genomic_sequence):
    result = []
    M = re.search('M', protein_sequence)
    if M:
        query = protein_sequence[M.start():]
        temp = open("temp.ORF", "w")
        print >>temp, '>blasting'
        print >>temp, query
        temp.close()
        cline = blastp(query="'temp.ORF'", db="DB.blast.txt",
                       evalue=0.01, outfmt=5, out=type + ".BLAST")
        os.system(str(cline))
        blast_out = open(type + ".BLAST")
        string = str(blast_out.read())
        DEF = re.search("<Hit_def>((E|L)\d)</Hit_def>", string)

I receive the error that blast_out=open(type+".BLAST") cannot find the specified file. This file gets created as part of the output of the program called by the os.system call. This usually takes ~30s or so to complete. However, When I try to run the program, it instantly gives the error I mention above.

I thought os.system() was supposed to wait for completion?
Should I force the wait somehow? (I do not want to hard code the wait time).

EDIT: I have ran the cline output in the command line version of the BLAST program. Everything appears to be fine.