# Computational biology at CSU

## DSCI 512: RNA-seq

### Questions?

examkey

This is an old revision of the document!

## Exam Key

exam_key.py
```def gc_content(sequence):
gc = 0
for nt in sequence:
if nt == 'G' or nt == 'C':
gc += 1
else:
continue
return gc/len(sequence)

def word_count(input_file):
try:
file_handle = open(input_file)
except:
return -1
lines = 0
chars = 0
with file_handle:
for line in file_handle:
line = line.rstrip()
chars += len(line)
lines += 1
return lines, chars

def matrix_mean(matrix):
l = []
for i in range(len(matrix)):
sum = 0
for n in range(len(matrix[0])):
sum += matrix[i][n]
l.append(sum/len(matrix[0]))
return l

def element_counter(some_list):
d = {}
for element in some_list:
d[element] = d.get(element, 0) + 1
return d

def motif_coordinates(sequence, motif):
for i in range(len(sequence) - len(motif) + 1):
if sequence[i:i+len(motif)] == motif:
return i+1, i+len(motif)

if __name__ == '__main__':
print(gc_content('ATTGCC')) # 0.5
print(word_count('test.txt')) # (2, 6)
print(matrix_mean([[1,2,3],[5,6,7]])) # [2.0, 6.0]
print(element_counter(['ATG', 'TAG', 'TTT', 'TAG', 'TTT'])) # {'TAG': 2, 'TTT': 2, 'ATG': 1}
print(motif_coordinates('ATGCTGTTAGCGA', 'CGA')) # (11, 13)
```