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How to deal with long list of return values and not face IndentationError

I have a function in Python that returns 5 items (I didn't develop the function so I cannot change it). If I want to give meaningful names to the return values, it will be a long line and it will exceed the 80 characters per line recommendation. So I wrote it like this:
encoded_en,
forward_h_en, forward_c_en,
backward_h_en, backward_c_en = encoder(embedding)
But then, I faced the indentation error:
File "<ipython-input-28-5947292b462a>", line 20
forward_h_en, forward_c_en
^
IndentationError: unexpected indent
What is the proper way to deal with such cases?

Use parentheses:
(encoded_en,
forward_h_en, forward_c_en,
backward_h_en, backward_c_en) = range(5)
print(encoded_en) # 0

ValueError in Python 3 code

I have this code that will allow me to count the number of missing rows of numbers within the csv for a script in Python 3.6. However, these are the following errors in the program:
Error:
Traceback (most recent call last):
File "C:\Users\GapReport.py", line 14, in <module>
EndDoc_Padded, EndDoc_Padded = (int(s.strip()[2:]) for s in line)
File "C:\Users\GapReport.py", line 14, in <genexpr>
EndDoc_Padded, EndDoc_Padded = (int(s.strip()[2:]) for s in line)
ValueError: invalid literal for int() with base 10: 'AC-SEC 000000001'
Code:
import csv
def out(*args):
print('{},{}'.format(*(str(i).rjust(4, "0") for i in args)))
prev = 0
data = csv.reader(open('Padded Numbers_export.csv'))
print(*next(data), sep=', ') # header
for line in data:
EndDoc_Padded, EndDoc_Padded = (int(s.strip()[2:]) for s in line)
if start != prev+1:
out(prev+1, start-1)
prev = end
out(start, end)
I'm stumped on how to fix these issues.Also, I think the csv many lines in it, so if there's a section that limits it to a few numbers, please feel free to update me on so.
CSV Snippet (Sorry if I wasn't clear before!):

The values you have in your CSV file are not numeric.
For example, FMAC-SEC 000000001 is not a number. So when you run int(s.strip()[2:]), it is not able to convert it to an int.
Some more comments on the code:
What is the utility of doing EndDoc_Padded, EndDoc_Padded = (...)? Currently you are assigning values to two variables with the same name. Either name one of them something else, or just have one variable there.
Are you trying to get the two different values from each column? In that case, you need to split line into two first. Are the contents of your file comma separated? If yes, then do for s in line.split(','), otherwise use the appropriate separator value in split().
You are running this inside a loop, so each time the values of the two variables would get updated to the values from the last line. If you're trying to obtain 2 lists of all the values, then this won't work.

Name not defined error python when reading file line by line

So, I am very new to python and I am not sure if my code is the most effective, but would still be very appreciative if someone could explain to me why my script is returning the "name not defined" error when I run it. I have a list of 300 gene names in a separate file, one name per line, that I want to read, and store each line as a string variable.
Within the script I have a list of 600 variables. 300 variables labeled name_bitscore and 300 labeled name_length for each of the 300 names.
I want to filter through the list based on a condition. My script looks like this:
#!/usr/bin/python
with open("seqnames-test1-iso-legal-temp.txt") as f:
for line in f:
exec("b="+line+"_bitscore")
exec("l="+line+"_length")
if 0.5*b <= 2*1.05*l and 0.5*b >= 2*0.95*l:
print line
ham_pb_length=2973
ham_pb_bitscore=2165
g2225_ph_length=3303
cg2225_ph_bitscore=2278
etc. for the length and bitscore variables.
Essentially, what I am trying to do here, is read line 1 of the file "seqnames-test1-iso-legal-temp.txt" which is ham_pb. Then I use wanted to use the exec function to create a variable b=ham_pb_bitscore and l=ham_pb_length, so that I could test if half the value of the gene's bitscore is within the range of double its length with a 5% margin of error. Then, repeat this for every gene, i.e. every line of the file "seqnames-test1-sio-legal-temp.txt".
When I execute the script, I get the error message:
Traceback (most recent call last):
File "duplicatebittest.py", line 4, in <module>
exec("b="+line+"_bitscore")
File "<string>", line 1, in <module>
NameError: name 'ham_pb' is not defined
I made another short script to make sure I was using the exec function correctly that looks like this:
#!/usr/pin/python
name="string"
string_value=4
exec("b="+name+"_value")
print(name)
print(b)
And this returns:
string
4
So, I know that I can use exec to include a string variable in a variable declaration because b returns 4 as expected. So, I am not sure why I get an error in my first script.
I tested to make sure the variable line was a string by entering
#!/usr/bin/python
with open("seqnames-test1-iso-legal-temp.txt") as f:
for line in f:
print type(line)
And it returned the line
<type 'str'>
300 times, so I know each variable line is a string, which is why I don't understand why my test script worked, but this one did not.
Any help would be super appreciated!

line is yield by the text file iterator, which issues a newline for each line read.
So your expression:
exec("b="+line+"_bitscore")
is passed to exec as:
b=ham_pb
_bitscore
Strip the output and that will work
exec("b="+line.rstrip()+"_bitscore")
provided that you move the following lines before the loop so variables are declared:
ham_pb_length=2973
ham_pb_bitscore=2165
g2225_ph_length=3303
cg2225_ph_bitscore=2278
Better: quit using exec and use dictionaries to avoid defining variables dynamically.

put #!/usr/bin/env python as the first line. See this question for more explanation.
As Jean pointed out, exec is not the right tool for this job. You should be using dictionaries, as they are less dangerous (search code injection) and dictionaries are easier to read. Here's an example of how to use dictionaries taken from the python documentation:
>>> tel = {'jack': 4098, 'sape': 4139}
>>> tel['guido'] = 4127
>>> tel
{'sape': 4139, 'guido': 4127, 'jack': 4098}
>>> tel['jack']
4098
>>> del tel['sape']
>>> tel['irv'] = 4127
>>> tel
{'guido': 4127, 'irv': 4127, 'jack': 4098}
>>> list(tel.keys())
['irv', 'guido', 'jack']
>>> sorted(tel.keys())
['guido', 'irv', 'jack']
>>> 'guido' in tel
True
>>> 'jack' not in tel
False
Here's a way I can think of to accomplish your goal:
with open("seqnames-test1-iso-legal-temp.txt") as f:
gene_data = {'ham_pb_length':2973, 'am_pb_bitscore':2165,
'g2225_ph_length':3303, 'cg2225_ph_bitscore':2278}
'''maybe you have more of these gene data things. If so,
just append them to the end of the above dictionary literal'''
for line in f:
if not line.isspace():
bitscore = gene_data[line.rstrip()+'_bitscore']
length = gene_data[line.rstrip()+'_bitscore']
if (0.95*length <= bitscore/4 <= 1.05*length):
print line
I take advantage of a few useful python features here. In python3, 5/7 evaluates to 0.7142857142857143, not your typical 0 as in many programming languages. If you want integer division in python3, use 5//7. Additionally, in python 1<2<3 evaluates to True, and 1<3<2 evaluates to False whereas in many programming languages, 1<2<3 evaluates to True<3 which might give an error or evaluate to True depending on the programming language.

why this python code is producing Runtime Error in ideone?

import sys
def func():
T = int(next(sys.stdin))
for i in range(0,T):
N = int(next(sys.stdin))
print (N)
func()
Here I am taking input T for for loop and iterating over T it gives Runtime error time: 0.1 memory: 10088 signal:-1 again-again . I have tried using sys.stdin.readline() it also giving same error .

I looked at your code at http://ideone.com/8U5zTQ . at the code itself looks fine, but your input can't be processed.
Because it is:
5 24 2
which will be the string:
"5 24 2"
this is not nearly an int, even if you try to cast it. So you could transform it to the a list with:
inputlist = next(sys.stdin[:-2]).split(" ")
to get the integers in a list that you are putting in one line. The loop over that.
After that the code would still be in loop because it want 2 integers more but at least you get some output.
Since I am not totally shure what you try to achieve, you could now iterate over that list and print your inputs:
inputlist = next(sys.stdin[:-2]).split(" ")
for i in inputlist
print(i)
Another solution would be, you just put one number per line in, that would work also
so instead of
5 24 2
you put in
5
24
2
Further Advice
on Ideone you also have an Error Traceback at the bottom auf the page:
Traceback (most recent call last):
File "./prog.py", line 8, in <module>
File "./prog.py", line 3, in func
ValueError: invalid literal for int() with base 10: '1 5 24 2\n'
which showed you that it can't handle your input

SPOJ: runtime error (NZEC)

I tried to do this problem at spoj.com, but I keep getting the error runtime error (NZEC). I code in python. I don't know why. Here is my code,
import sys
def unique(lines, exact=True):
for L in lines:
if L.count('#') != 1 and exact:
return False
if L.count('#') > 1 and not exact:
return False
return True
def resolve(N, lines):
diags = [
[lines[i][i+j] for i in range(max(0, -j), min(N, N-j))]
for j in range(-N+1, N)]
anti_diags = [
[lines[i][N-1 -(i+j)] for i in range(max(0, -j), min(N, N-j))]
for j in range(-N+1, N)]
if unique(lines) and unique(zip(*lines)) and unique(diags, False) and unique(anti_diags, False):
return "YES"
return "NO"
input_file = sys.stdin
output_file = sys.stdout
T = int(raw_input())
for i in range(1, T + 1):
n = int(raw_input())
lines = []
for _ in range(n):
line = raw_input().strip()
lines.append(list(line))
print resolve(n, lines)
It works fine locally with input like:
2
3
..#
#..
.#.
4
.#..
...#
#...
..#.

When I run your code, I get the following:
$ python spoj.py < input
Traceback (most recent call last):
File "spoj.py", line 38, in <module>
print resolve(n, lines)
File "spoj.py", line 15, in resolve
for j in range(-N+1, N)]
IndexError: list index out of range
That's the runtime error you're getting. But the problem is actually in this part:
for _ in range(n):
line = raw_input().strip()
lines.append(list(line))
print resolve(n, lines)
Since the print statement is indented, your program reads a single line, appends to line and calls resolve before reading the following lines. After removing the extra indent, it works fine on my computer.
There's plenty of room to further improve this program, both in style and logic. Let me know if you would like some further advice.
EDIT:
You mentioned in the comments that this indentation problem was a copypasting error. In that case, as sp1r pointed out in his comment, it's most likely that, as a comment in the problem's page suggests, the input used by the online judge is malformed.
In that case, you have to do more rigorous parsing of the input, as it may not be formatted as the example input suggests. That is, instead of:
2
3
..#
#..
.#.
(etc)
you could have something more like:
2 3
..#
#.. .#.
(etc)
That might break your code because it assumes whoever posted the problem was competent enough to make an input that looks like the example. That is not always the case in SPOJ, a lot of the input files is malformed and you can find other cases where malformed input causes otherwise correct programs to fail.

Spoj does not use sys and sys.stdin and sys.stdout. use raw_input() and print.
"I am on windows not on linux. I simply change this line to switch to console modes for tests."
In any language and in any os, these works fine.
#for Python
spoj.py < input.txt > output.txt
#If you are using C/C++, for any EXE file
spoj.exe < input.txt > output.txt
Spoj will nether test this in your computer nor using any UI. They will test your code, in a "console" and it might be a linux / any-OS machine. Use this input / output to Test your code.