Mixed starting strain to one ending strain

#|*******************************************************************************
#| Functions that handle mixed starting strain to one ending strain
#|*******************************************************************************


def make_extra_plates():
    '''
    |       user input -> file
    |
    |       Returns a file containing multiplexed plate or plates need to run
    |       that includes all the primers missing in the first file but present
    |       in the second file.
    |
    |       Preconditions:
    |           files
    |               .txt files
    |
    |               example snippet of one input file
    |               1 D15mit252F D6mit224V D15mit59N none
    |               2 D1mit440F D1mit236V D16mit107N none
    |
    |               no blank lines in the file
    |
    |           python 3 needs to be used
    |
    |       Example use of this function:
    |       A comstomer comes to start a speed congenics project however the
    |       starting strain of the project is mixed.  For example the starting
    |       strain is 129 and C3H combined.  The customer wants to cross this
    |       mouse onto the B6 background.  Therefore the best approach would be
    |       to run a full 129XB6 screen (1st input asked for) and then run the
    |       primers that are present in the B6XC3H screen and not in the 129XB6
    |       screen. The second screen asked for will be the B6XC3H screen.

    '''

# get input of locations of files
    full_screen_running = input('''Please enter the location of the full
screen be you running: ''')
    other_strain = input('''Plese enter the location of the other plate mat
you are wishing to inducde: ''')

# output_list will now equall a list of all primers not in file1 but in file2
    extra_primers_needed  = primers_missing_from_plate_mat(full_screen_running,other_strain)

# seperates all primers into nested fluorescence lists
    fluoro_list = make_seperate_lists(extra_primers_needed)

# remove all the empty lists.
    empties_removed = remove_empties(fluoro_list)

# multiplex all the primers
    multiplexed = multiplex_primers(empties_removed)

# get input of where is the output_file is
    to_file = input('''Please enter the location of the .txt file you would
like the multiplexed extra plates writen to: ''')

# write all the primers to a file
    write_extra_primer_layout(multiplexed, to_file)

    print('Complete!  The extra primers you need are located at', to_file)

def primers_missing_from_plate_mat(first_screen_mat, extra_primer_mat):
    '''
    |       (file, file) -> list
    |
    |       Return a list of primers which are not in the first file but are
    |       present in the second file.
    |
    |       first_screen_mat example
    |       1 D15mit252 F D6mit224 V D15mit59 N none
    |       2 D1mit440 F D1mit236 V D16mit107 N none
    |
    |       extra_primer_mat example
    |       1 D15mit252 F D6mit224 V D15mit59 N none
    |       2 D19mit91 V D1mit236 V D16mit107 N none
    |
    |       list output example
    |       ['D19mit91 V']

    '''
    with open(first_screen_mat, 'r') as sf:
        with open(extra_primer_mat, 'r') as of:
            line = sf.readline()
            sf_list = []
            while line != '':

                line = line.strip().split()


                for s in line:
                    if s != 'none' and not s.isdigit():
                        sf_list.append(s)

                line = sf.readline()


            line = of.readline()
            output_list = []

            while line != '':
                line = line.strip().split()

                for s in line:
                    if s not in sf_list and s != 'none' and not s.isdigit():

                        output_list.append(s)


                line = of.readline()

    print('\nThe full screen you will be running includes', len(sf_list), 'primers\n')

    print('The extra plate or plates includes', len(output_list), 'primers\n')

    print('Therefore the total number of primers used for this project is',
          (len(sf_list) + len(output_list)), '\n')
    return output_list

def make_seperate_lists(mixed_list):
    '''
    |       (list) -> list
    |
    |       Returns a nested 2D list of strings.  Each nested list is seperated into
    |       primer fluorescence. Therefore there are 4 nested lists.  One for FAM,
    |       one for Vic, one for Ned, and one for Pet in that order.  Each list will
    |       be created.  However, somelists might be empty such as the Pet list
    |       in the example below.
    |
    |       example input list:
    |       ['D19mit91F', 'D13mit275V', 'D9mit90V', 'D14mit95F', 'D9mit182F',
    |       'D11mit231N']
    |
    |       example output_list:
    |       [['D19mit91F', 'D14mit95F', 'D9mit182F'], ['D13mit275V', 'D9mit90V'],
    |       ['D11mit231N'], []]


    '''
    l = mixed_list
    F_list = []
    V_list = []
    N_list = []
    P_list = []
    for s in l:
        if s[-1] == 'F':
            F_list.append(s)
        elif s[-1] == 'V':
            V_list.append(s)
        elif s[-1] == 'N':
            N_list.append(s)
        elif s[-1] == 'P':
            P_list.append(s)

    new_list = [F_list, V_list, N_list, P_list]
    return new_list

def remove_empties(fluro_seperated_list):
    '''
    |       (2D list) -> 2D list
    |
    |       Returns a nested 2D list that contains no empty lists.
    |
    |       Example 2D_list_input:
    |       [['D19mit91F', 'D14mit95F', 'D9mit182F'], ['D13mit275V', 'D9mit90V'],
    |       ['D11mit231N'], []]
    |
    |       Example 2D_list_output:
    |       [['D19mit91F', 'D14mit95F', 'D9mit182F'], ['D13mit275V', 'D9mit90V'],
    |       ['D11mit231N']]
    '''
    list2 = [x for x in fluro_seperated_list if x]
    return list2

def multiplex_primers(fluro_seperated_list_no_empties):
    '''
    |       (2D list) -> 2D list
    |
    |       Returns a list where each primer is multiplexed with one other primer of
    |       a different fluorescence.
    |
    |       Example input_list:
    |       [['D19mit91F', 'D14mit95F', 'D9mit182F'], ['D13mit275V', 'D9mit90V'],
    |       ['D11mit231N']]
    |
    |       Example output_list:
    |       [['D19mit91F', 'D13mit275V'], ['D14mit95F', 'D9mit90V'],
    |       ['D9mit182F', 'D11mit231N']]

    '''

    answer = []

    new_list = fluro_seperated_list_no_empties

    while len(new_list[0]) > 0 and len(new_list[1]) > 0:
        answer.append([new_list[0][0], new_list[1][0]])
        del new_list[0][0], new_list[1][0]

        new_list = remove_empties(new_list) #remove empty lists every iteration

        if len(new_list) == 0: #if length is 0, our work is done
            break
        if len(new_list) == 1: #if length is 1, we need to append remaining numbers as lists with length 1

            for i in new_list[0]:
                answer.append([i])
            break

    return answer


def write_extra_primer_layout(list_of_multiplexed_primers, to_file):
    '''
    |       (2D list) -> file
    |
    |       Returns a file  that contains primers in the lists in plate format.  A
    |       number in the file counts up to 12 and restarts for the next plate.
    |
    |       Example input_list
    |       [['D19mit91F', 'D13mit275V'], ['D14mit95F', 'D9mit90V'],
    |       ['D9mit182F', 'D11mit231N'], ['D19mit91F', 'D13mit275V'],
    |       ['D14mit95F', 'D9mit90V'], ['D9mit182F', 'D11mit231N'],
    |       ['D19mit91F', 'D13mit275V'], ['D14mit95F', 'D9mit90V'],
    |       ['D9mit182F', 'D11mit231N'],['D19mit91F', 'D13mit275V'],
    |       ['D14mit95F', 'D9mit90V'], ['D9mit182F', 'D11mit231N'],
    |       ['D19mit91F', 'D13mit275V'], ['D14mit95F', 'D9mit90V'],
    |       ['D9mit182F', 'D11mit231N'], ['D19mit91F', 'D13mit275V'],
    |       ['D14mit95F', 'D9mit90V'], ['D9mit182F', 'D11mit231N'],
    |       ['D19mit91F', 'D13mit275V'], ['D14mit95F', 'D9mit90V'],
    |       ['D9mit182F', 'D11mit231N']]
    |
    |       Example out_put file:
    |       1 D19mit91F D13mit275V
    |       2 D14mit95F D9mit90V
    |       3 D9mit182F D11mit231N
    |       4 D19mit91F D13mit275V
    |       5 D14mit95F D9mit90V
    |       6 D9mit182F D11mit231N
    |       7 D19mit91F D13mit275V
    |       8 D14mit95F D9mit90V
    |       9 D9mit182F D11mit231N
    |       10 D19mit91F D13mit275V
    |       11 D14mit95F D9mit90V
    |       12 D9mit182F D11mit231N
    |
    |       1 D19mit91F D13mit275V
    |       2 D14mit95F D9mit90V
    |       3 D9mit182F D11mit231N
    |       4 D19mit91F D13mit275V
    |       5 D14mit95F D9mit90V
    |       6 D9mit182F D11mit231N
    |       7 D19mit91F D13mit275V
    |       8 D14mit95F D9mit90V
    |       9 D9mit182F D11mit231N
    '''

    in_list = list_of_multiplexed_primers
    with open(to_file, 'w') as tf:

      num = 1
      for i in in_list:
        if num == 12:
            tf.write(str(num)+ ' ' +(' '.join(i)) + ' ' +'\n\n')
            num = 1

        else:
            tf.write(str(num)+ ' ' +(' '.join(i)) + ' ' +'\n')
            num = num + 1