Python Loops for bioinformatics

# Title: Looping through elements in Python
# In Python 2, there are 2 ways to loops through a list.

# The first method loops through all elements and does not store the position of the element
some_unknown_seqeunce = 'BACKTOTHEFUTURE'

#using the list we created above, we can print out every letter (without knowing its position!!!)
print '--- Method 1 --'
for letter in some_unknown_seqeunce:
    print letter

# if we want to access the index or position of the letters we have to use a trick
print "--- Method 2 ---"
for position in range(len(some_unknown_seqeunce)):
    print position, ' - ', some_unknown_seqeunce[position]

# Sometimes you want to quickly print a list, other times you need the position of elements in the list
# Right now we just want to check what letters are in our shortened amino acids list
print '--- Comparing Methods ---'
short_amino_acids = ['A','C','D','E','F','G','H','I','J','K','L','M']

# print all letters that are amino acids
print '--- No index needed ---'
for letter in some_unknown_seqeunce:
    if letter in short_amino_acids:
        print letter

# Many biological sequnces come in pairs, triplets, or larger groups. Check every 3rd amino acid, and print the position.
# NOw and idex is needed
print '--- Now an index is needed ---'
for position in range(len(some_unknown_seqeunce)):
    if (position % 3 == 0) and (some_unknown_seqeunce[position] in short_amino_acids): # google modulo if you dont understand this
        print position, ' - ', some_unknown_seqeunce[position]

Python Fiddle

Python Cloud IDE