file.py

def bot_login():
    print "Loggin in..."
    r = praw.Reddit(username = config.username,
            password = config.password,
            client_id = config.client_id,
            client_secret = config.client_secret,
            user_agent = "phylohelper v0.1")
    print "Logged in!"

    return r

def run_bot(r, comments_replied_to):
    print "Obtaining 10 comments..."

    for comment in r.subreddit('whatsthissnaketest').comments(limit=10):
# we still want all these checks other than the one checking if the keyword is in the comment
        if comment.author.name.lower() in list_of_names and comment.id not in comments_replied_to and comment.author != r.user.me() and datetime.utcfromtimestamp(comment.created_utc) > startTime:
# now if it's a good comment, let's loop over all of our words
            for species in specieslist:
# check if this word is in the comment
                if "*"+species+"*" in comment.body:
                    print "String with \"+ species""\" found in comment " + comment.id
# assuming your text file is the species name
                    with open(species + ".txt", "r") as f:
                        comment_reply = f.read()
                        comment.reply(comment_reply + "\n\n" + sig)
                        print "Replied to comment " + comment.id

                    comments_replied_to.append(comment.id)

                    with open ("comments_replied_to.txt", "a") as f:
                        f.write(comment.id + "\n")

            # assuming you only want to reply once to each comment, even if it has multiple keywords, so let's break out of the loop
            #break

    # checking if there's brackets in the title with text in them is a little bit tricky to do normally, so we're going to use something called a regex
    # this is basically a fancy way of finding a certain string inside another string and it lets us do all kinds of fancy stuff like use wildcards
    for submission in r.subreddit('whatsthissnaketest').new(limit=10):
        # we're doing a couple things here. First we're calling the function re.findall, which is our fancy search function. We pass in our regex and the submission title
        # The regex is '\[.+\]'. We want to first find [, but that already has a special meaning in regex, so we need to escape it with the '\'. Then '.' means any character at all
        # and we modify it with '+', which means at least one, but then any number. Then we close it with another '\]' bracket. So something like '[test]' matches
        # but '[]' doesn't. And '[test' doesn't. And no brackets at all doesn't either. This function returns a list of the matches, so we can check the length of the list.
        # If that length is 0, there are no matches, and we should reply with our comment.
        if len(re.findall('\[.+\]', submission.title)) == 0:
            submission.reply("Please provide a geographic location")


    print "Sleeping for 30 seconds..."
    #Sleep for 30 seconds...
    time.sleep(30)


def get_saved_comments():
    if not os.path.isfile("comments_replied_to.txt"):
        comments_replied_to = []
    else:
        with open("comments_replied_to.txt", "r") as f:
            comments_replied_to = f.read()
            comments_replied_to = comments_replied_to.split("\n")
            comments_replied_to = filter(None, comments_replied_to)

    return comments_replied_to

r = bot_login()
comments_replied_to = get_saved_comments()
print comments_replied_to

while True:
    run_bot(r, comments_replied_to)