Refactored dodo.py (see https://groups.google.com/d/msg/python-doit/aE6pwa7_uBU/cXBDFDQPAgAJ)

dodo.py

import os


def task_one():
    def create_cmd_string(a, b, target):
        return "echo a: %s b: %s  > %s" % (a, b, target)

    with open("list_of_input_filenames.txt") as f:
        fnames = [line.strip() for line in f.readlines() if line]
    for a in fnames:
        for b in fnames:
            a_name_tail = os.path.basename(a).split("_")[1]
            b_name_tail = os.path.basename(b).split("_")[1]
            target = "output/output_%s_%s.out" % (a_name_tail, b_name_tail)
            yield {
                'name': "%s_%s" % (a_name_tail, b_name_tail),
                'actions': [create_cmd_string(a, b, target)],
                'file_dep': [a, b],
                'targets': [target],
                'clean': True
            }

dodo_org.py

import os

def task_1():
        def run_task1(a,b,targets):
                os.system("programmename -i %s -o %s  > %s"%(a,b,targets[0]))
                return

        LIST=open("list_of_input_filenames.txt",'r')
        LIST=LIST.readlines()
        for a in LIST:
                a=a.rstrip()
                for b in LIST:
                        b=b.rstrip()
                        if os.path.isfile("output/output_%s_%s.out"%(a.split("/")[-1].split("_")[1],b.split("/")[-1].split("_")[1])) == False:
                                yield {'name':"task1_%s_%s"%(a.split("/")[-1].split("_")[1],b.split("/")[-1].split("_")[1]),
                                       'actions':[(run_task1,[a,b])],
                                       'file_dep':[a,b],
                                       'targets':["output/output_%s_%s.out"%(a.split("/")[-1].split("_")[1],b.split("/")[-1].split("_")[1])]
                                      }