Bash style process substitution with Python's Popen

Question

In Bash you can easily redirect the output of a process to a temporary file descriptor and it is all automagically handled by bash like this:

$ mydaemon --co         


        

Answer 1

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 os
import tempfile
from subprocess import check_output

with tempfile.NamedTemporaryFile() as file:
    file.write(generate_kmers(3))
    file.delete = False

try:
    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_call

with 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 os
import shutil
import tempfile
from contextlib import contextmanager
from subprocess import Popen, PIPE

@contextmanager
def 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()