Bash style process substitution with Python's Popen

If pram_axdnull understands "-" convention to mean: "read from stdin" then you could:

p = Popen(["pram_axdnull", str(kmer), input_filename, "-"],          stdin=PIPE, stdout=PIPE)output = p.communicate(generate_kmers(3))[0]

If the input is generated by external process:

kmer_proc = Popen(["generate_kmers", str(kmer)], stdout=PIPE)p = Popen(["pram_axdnull", str(kmer), input_filename, "-"],          stdin=kmer_proc.stdout, stdout=PIPE)kmer_proc.stdout.close()output = p.communicate()[0]

If pram_axdnull doesn't understand "-" convention:

import osimport tempfilefrom subprocess import check_outputwith tempfile.NamedTemporaryFile() as file:    file.write(generate_kmers(3))    file.delete = Falsetry:    p = Popen(["pram_axdnull", str(kmer), input_filename, file.name],              stdout=PIPE)    output = p.communicate()[0]    # or    # output = check_output(["pram_axdnull", str(kmer), input_filename,                              file.name])finally:    os.remove(file.name)

To generate temporary file using external process:

from subprocess import check_callwith tempfile.NamedTemporaryFile() as file:    check_call(["generate_kmers", str(kmer)], stdout=file)    file.delete = False

To avoid waiting for all kmers to be generated i.e., to write/read kmers simultaneously, you could use os.mkfifo() on Unix (suggested by @cdarke):

import osimport shutilimport tempfilefrom contextlib import contextmanagerfrom subprocess import Popen, PIPE@contextmanagerdef named_pipe():    dirname = tempfile.mkdtemp()    try:        path = os.path.join(dirname, 'named_pipe')        os.mkfifo(path)        yield path    finally:        shutil.rmtree(dirname)with named_pipe() as path:    p = Popen(["pram_axdnull", str(kmer), input_filename, path],              stdout=PIPE) # read from path    with open(path, 'wb') as wpipe:        kmer_proc = Popen(["generate_kmers", str(kmer)],                          stdout=wpipe) # write to path    output = p.communicate()[0]    kmer_proc.wait()