I'm looking to run a number of Fasta files simultaneously using local blast for a pipeline. Im using biopython to read in my input file and parse through for a specified number of sequences e.g. 1000 if the file is larger i batch it out into segments of 1000. But i'm now looking for a way be able to run each file through local blast rather than one at a time and then concatenating all the output files i receive for post-blast parsing by E-value.

def batch_iterator(iterator, batch_size):#generator function for splitting large files
    entry = True  # Make sure we loop once
    while entry:
        batch = []
        while len(batch) < batch_size:
            try:
                entry = iterator.__next__()
            except StopIteration:
                entry = None
            if entry is None:
                # End of file
                break
            batch.append(entry)
        if batch:
            yield batch 

counter =0
for record in SeqIO.parse(Input_file,'fasta'):# pasrse input file for sequence #
    counter +=1
    if counter > 10:#if input file has more than 10 seqs file is batched  
        record_iter=SeqIO.parse(open(Input_file),"fasta")
        for i, batch in enumerate(batch_iterator(record_iter, 10)):
            filename = "batch_%i.fasta" % (i + 1)
            with open(filename, "w") as handle:
                count = SeqIO.write(batch, handle, "fasta")
            print("Write %i records to %s" % (count, filename))      
    else:
        continue

What would be the best way to automate this so i grab all my batch files and run them through local blast? Would i have to use ./blastp -db a_database -query queryfile.fasta -out blastoutpu.tsv -outfmt 6 for individual file name using the os(command) in my script or is there a simpler way?