Comparing a list of known animals to a master list of animals
This is the sort of thing that Python is really good at.  Your code seems like it functions, but it will be very inefficient for large data sets. For each input value you have to check every line in the the master list -- and the way you have it set up here you're going to read the master list off disk for each input value as well, so it will be really slow.

The first step obvious fix is to load the master list into memory and keep it around for the duration of a session.  This is a fairly simple change to your existing code.  First, change your pull_lines so it returns a dictionary instead of a list:

def pullLines(file_input):
    '''returns a dictionary of the entries in &lt;file_input&gt; keyed by the first item in each line'''
    master_dict = {}
    with open(file_input,'rU') as info:
        for eachline in info.readlines():
            tokens = eachline.split()
            master_dict[tokens[0]] = tokens[1:]


Then, you move pull lines out of the inner loop:

lookup = pull_lines(path_to_file)
with open(results_list,"w+") as output:
    output.write(getHeader(master_list))
    for item in pullIDs(known_stars):
        if item in lookup:
            output.write(lookup[item])


This has a couple of advantages

1) not hitting the disk for every query will be much faster

2) the dictionary lookup faction is much faster than straight for loop comparison, since the dictionary uses hashed values instead of more expensive string compares.

As an aside, you should look into readlines, which the usual pythonic way of reading text files with info on lines.

For the longer term this is a great application for Python's built in database functionality (with the sqllite module). You could convert your existing text files into a sqllite database and then your lookups can be much more flexible and precise ('find spectrum and power for stars with id > X and &lt; Y' sort of thing).  You probably also want to set this file up so you could call it from the command line, which would involve using the argparse module to grab command line arguments and out them into known_stars, master_list and output_file