Python bioinformations 101

base_counts.py

dna3 = 'ACGACGGATACGCGGGAGCTATTCATCTGTGTTGAGAAACACCGGAGAACTTATTGGTCTGTCAAGATTGCGACTGTGGTATAGCTCACCCGGTCGCGGCTTTCTAGT' \
       'TAGTGGCCAGCTCCCGTGTATTTGGAAGCTGAGAGAAGGACCCCTGTGGTTCGAATCAGCTCACGAGCGCTGGCACACCGCAATCAGCCGGCTAATAAAATTCGTACG' \
       'GACTGCCCCACACAAGAAGACGGTAAATTTATCAACACTATAGTTGCTATACACCAGGAGCGAGCGTAAATTTGTAGCGGTCAGATTAACTTGCTGGGAACGAACCAT' \
       'TGTCGCCCTCTGCAGCAAGTTAGTTGGCATCATTGGTACTGCCCTTCACTGGTAGCAGCTCCCCCTGTAATATATCCGTGGCCACTATTCAAGGGCTCAAATAGGCGA' \
       'CCCAGAGACCATTATAGGCGGTACAGCGCTGGTAGGTTTGCCTGGGCAGATATCGTTAGCCCCTTCTGCGCGCTATAAGATAGCGAAGGATAATTCTGCGGGACCA' \
       'TGGTCGTCTCCTAACCTCAGGGTGGGATTCCTGGCAGGTGGACCGGGCGCGCATCGAGAGCATTCGGGGTTCCTACCAGCCAGGGAAATCGGGTCGACCACTAGGCAA' \
       'TGAGCGGCTCACACCGATTTTCTTAAGAGACGTAACAAAGCCCGCATTAACGGCTGGAGTGAATCACCGTACGACTACCTAAGCCTCATTGGGATCCACTGTAAACCC' \
       'CTTCGCCGGTGTTGGGTGTCCGCAACGCCTCTGCTTTTTGCGTACAGTCGGCGTGGTGGAGTCCGCGGCCATACTGGCGGTTGGTTTGTAGAACAGTGTAACGACGTG' \
       'TGTCACTGCCCCCCGTAGCTTCTATTGCCCTGTTTGGGAGGTTCTATAGGGGTTACAGAGTAGTTTTAAGTTTTAGCACGACAGCACCAGTATTGCCAGTGACGCCGT' \
       'TGAGGCCGCAAAAGTGATTAACCCCCGTGGGACCGGATACGTTCCCAGCGGCAATCCTTGTCTTACCGCCGGACTGCGGAGCGAAGGGAGAAGTAACCGTGGTAATTA'

dna4 = 'CAGAGCAATGTCTGTTAGATAATCTCTCGTCTGGATAGCGAGAAGTTTCCGGAAGACGATTGTTTCCAACGAAAGGGCTGATAACTACACTCTGTCGCGCTTCTTTCG' \
       'TGTTCGCCAAGGGCACATTGGTTTAAAAGTGATCTCGAGAGACGTTTTCCTGACTTGTTGTGTTATATCAACGTAACTTTTAAGTCATATTTTCTCCCTACCCCAGAC' \
       'TAGACGGGTTCCTTTCATCGTCCACCGAGTTGCTTACGAGCAUGACACTTAGCCGGGGAAAAGTTCGCAATTCCGCGACAGCGTCAGGTGTCAAACAGATCCAAGCGA' \
       'AGGCCGCCGTGTAACGGAGAATTGTGGGCGCAGTCAAATAGCTAATTATTGGGAAAGGCCAAGTGGAGTCCGTCAGCGGAACAGCCTGGGCGGACGCGCTGCCGCTCG' \
       'TTCACCTCGCCTGCCTTCGTGTTGGGGACCGGATACGTTCCCAGCGGCAATCCTTGTCTTACCGCCGGACTGCGGAGCGAAGGGAGAAGTAACCGTGGTAATTAGCGA' \
       'GAGACCGTTGAGGCGCGGGGCGATCCGCCCTTGAGTGGACTCCAAACACATTCGACGAAGGGGTGGGAACATAAGTTAATTGGAGGGTCGGGGAAGTCCCACGCCCGG' \
       'TCCCTACATGATTGCACATAGTTCGTTCACCAACGGGCGATCTTCCTCACACTAGAGGAACGAGTAGTACTCCAGACATTGAGTCAGTTGCAGACCAAGTGGAGGGAA' \
       'CGATTTTTAUGGGCCGCTCAGGTACTAGTGCTAGACCCTACAAACGGCACTGGTGACCCGCTCCCGAGTTTGCGCTGTTACGTGTCCCTTAAAGTATACTTCGATCCT' \
       'AACATCGCGGCCATACGACGCTTAAATATTTCACCAGTTGTGTTTCGCGCAUGGAGTTGTTCTGTGTTATCGGCGAGTCTCCATTGCACGTCATCAACTAAAAACCAC' \
       'GGCCACACAGACATGCCTTGATTCTTCCCGCGACGGTAGGTTTGCCTGGGCAGATATCGTTAGCCCCTTCTGCGCGCTATAAGATAGCGATAGTAGGTTTAACTATCA'

print(len(dna3))

# how many A, C, G, and T are in dna3?
# what about dna4?
# can you write a function?
# and thinking more generally - what if you don't know what letters there are?
#

# Creating variables
a_count = 0
c_count = 0
g_count = 0
t_count = 0

for base in dna3:
    if base == 'A':
        a_count += 1
    if base == 'C':
        c_count += 1
    if base == 'G':
        g_count += 1
    if base == 'T':
        t_count += 1

print(a_count, c_count, g_count, t_count)

# creating a dictionary of counts
# how could you generate this from the text?
base_counts = {'A': 0, 'C': 0, 'G': 0, 'T': 0}

# work with dictionary keys and values
for base in dna3:
    if base == 'A':
        base_counts['A'] += 1
    if base == 'C':
        base_counts['C'] += 1
    if base == 'G':
        base_counts['G'] += 1
    if base == 'T':
        base_counts['T'] += 1

print(base_counts)

base_counts = {'A': 0, 'C': 0, 'G': 0, 'T': 0}

# but now we have a dictionary, we can make this much more general
for base in dna3:
    base_counts[base] += 1

print(base_counts)

# Question: how could you generate this intial dictionary from the text?
# Questions: can you put the counting code into a function? 

dna.py

# Example of real-world use of Python string manipulation - DNA analysis
#
# DNA is made of ATGC
#
# A-T are always paired
# G-C are always paired
#
# So if you have a sequence of one side of a DNA molecule, can you use Python to generate the other side?
#


dna1 = 'ACCAGTACCAGTGT'
dna2 = 'GTACACCAGGTCTA'

# Remember
# A pairs with T   and     T pairs with A
# C pairs with G   and     G pairs with C

# so for dna1, it begins ACCA... so output string will start TGGT...

# In DNA, the A, T, C, G are codes for generating proteins
#   you are made of 100's of different kinds of proteins.
# Most of your DNA doesn't appear to make proteins - only about 1% of it encodes protein.
# A part of DNA that encodes a protein is called a gene So how do you find which parts do,
# or where are your genes in your DNA?
#
# So biologist are interested in where certain codes are. One code is ATG and this
# is called a 'start codon' and that means 'start making a protein here'
#
# Does string 1 have any genes in it?
# Does string 2 have any genes in it?
#
# If so, what's the index of where that gene is?

dna3 = 'ACGACGGATACGCGGGAGCTATTCATCTGTGTTGAGAAACACCGGAGAACTTATTGGTCTGTCAAGATTGCGACTGTGGTATAGCTCACCCGGTCGCGGCTTTCTAGT' \
       'TAGTGGCCAGCTCCCGTGTATTTGGAAGCTGAGAGAAGGACCCCTGTGGTTCGAATCAGCTCACGAGCGCTGGCACACCGCAATCAGCCGGCTAATAAAATTCGTACG' \
       'GACTGCCCCACACAAGAAGACGGTAAATTTATCAACACTATAGTTGCTATACACCAGGAGCGAGCGTAAATTTGTAGCGGTCAGATTAACTTGCTGGGAACGAACCAT' \
       'TGTCGCCCTCTGCAGCAAGTTAGTTGGCATCATTGGTACTGCCCTTCACTGGTAGCAGCTCCCCCTGTAATATATCCGTGGCCACTATTCAAGGGCTCAAATAGGCGA' \
       'CCCAGAGACCATTATAGGCGGTACAGCGCTGGTAGGTTTGCCTGGGCAGATATCGTTAGCCCCTTCTGCGCGCTATAAGATAGCGAAGGATAATTCTGCGGGACCA' \
       'TGGTCGTCTCCTAACCTCAGGGTGGGATTCCTGGCAGGTGGACCGGGCGCGCATCGAGAGCATTCGGGGTTCCTACCAGCCAGGGAAATCGGGTCGACCACTAGGCAA' \
       'TGAGCGGCTCACACCGATTTTCTTAAGAGACGTAACAAAGCCCGCATTAACGGCTGGAGTGAATCACCGTACGACTACCTAAGCCTCATTGGGATCCACTGTAAACCC' \
       'CTTCGCCGGTGTTGGGTGTCCGCAACGCCTCTGCTTTTTGCGTACAGTCGGCGTGGTGGAGTCCGCGGCCATACTGGCGGTTGGTTTGTAGAACAGTGTAACGACGTG' \
       'TGTCACTGCCCCCCGTAGCTTCTATTGCCCTGTTTGGGAGGTTCTATAGGGGTTACAGAGTAGTTTTAAGTTTTAGCACGACAGCACCAGTATTGCCAGTGACGCCGT' \
       'TGAGGCCGCAAAAGTGATTAACCCCCGTGGGACCGGATACGTTCCCAGCGGCAATCCTTGTCTTACCGCCGGACTGCGGAGCGAAGGGAGAAGTAACCGTGGTAATTA'

dna4 = 'CAGAGCAATGTCTGTTAGATAATCTCTCGTCTGGATAGCGAGAAGTTTCCGGAAGACGATTGTTTCCAACGAAAGGGCTGATAACTACACTCTGTCGCGCTTCTTTCG' \
       'TGTTCGCCAAGGGCACATTGGTTTAAAAGTGATCTCGAGAGACGTTTTCCTGACTTGTTGTGTTATATCAACGTAACTTTTAAGTCATATTTTCTCCCTACCCCAGAC' \
       'TAGACGGGTTCCTTTCATCGTCCACCGAGTTGCTTACGAGCAUGACACTTAGCCGGGGAAAAGTTCGCAATTCCGCGACAGCGTCAGGTGTCAAACAGATCCAAGCGA' \
       'AGGCCGCCGTGTAACGGAGAATTGTGGGCGCAGTCAAATAGCTAATTATTGGGAAAGGCCAAGTGGAGTCCGTCAGCGGAACAGCCTGGGCGGACGCGCTGCCGCTCG' \
       'TTCACCTCGCCTGCCTTCGTGTTGGGGACCGGATACGTTCCCAGCGGCAATCCTTGTCTTACCGCCGGACTGCGGAGCGAAGGGAGAAGTAACCGTGGTAATTAGCGA' \
       'GAGACCGTTGAGGCGCGGGGCGATCCGCCCTTGAGTGGACTCCAAACACATTCGACGAAGGGGTGGGAACATAAGTTAATTGGAGGGTCGGGGAAGTCCCACGCCCGG' \
       'TCCCTACATGATTGCACATAGTTCGTTCACCAACGGGCGATCTTCCTCACACTAGAGGAACGAGTAGTACTCCAGACATTGAGTCAGTTGCAGACCAAGTGGAGGGAA' \
       'CGATTTTTAUGGGCCGCTCAGGTACTAGTGCTAGACCCTACAAACGGCACTGGTGACCCGCTCCCGAGTTTGCGCTGTTACGTGTCCCTTAAAGTATACTTCGATCCT' \
       'AACATCGCGGCCATACGACGCTTAAATATTTCACCAGTTGTGTTTCGCGCAUGGAGTTGTTCTGTGTTATCGGCGAGTCTCCATTGCACGTCATCAACTAAAAACCAC' \
       'GGCCACACAGACATGCCTTGATTCTTCCCGCGACGGTAGGTTTGCCTGGGCAGATATCGTTAGCCCCTTCTGCGCGCTATAAGATAGCGATAGTAGGTTTAACTATCA'

print(dna4.upper())
# why using the \ line extender and not triple-quoted strings?

dna_string_start.py

# How many A, C, G, T characters are in this string?
# 
# if 
#     
# dna = 'CGATC'
# 
# We could count easily, there are 
#    1 A
#    2 C 
#    1 G
#    1 T
#
# What about a longer string? 
# 
# Create a much long example string. How would you count the number of each character? 

dna = 'ACGACGGATACGCGGGAGCTATTCATCTGTGTTGAGAAACACCGGAGAACTTATTGGTCTGTCAAGATTGCGACTGTGGTATAGCTCACCCGGTCGCGGCTTTCTAGT' \
       'TAGTGGCCAGCTCCCGTGTATTTGGAAGCTGAGAGAAGGACCCCTGTGGTTCGAATCAGCTCACGAGCGCTGGCACACCGCAATCAGCCGGCTAATAAAATTCGTACG' \
       'GACTGCCCCACACAAGAAGACGGTAAATTTATCAACACTATAGTTGCTATACACCAGGAGCGAGCGTAAATTTGTAGCGGTCAGATTAACTTGCTGGGAACGAACCAT' \
       'TGTCGCCCTCTGCAGCAAGTTAGTTGGCATCATTGGTACTGCCCTTCACTGGTAGCAGCTCCCCCTGTAATATATCCGTGGCCACTATTCAAGGGCTCAAATAGGCGA' \
       'CCCAGAGACCATTATAGGCGGTACAGCGCTGGTAGGTTTGCCTGGGCAGATATCGTTAGCCCCTTCTGCGCGCTATAAGATAGCGAAGGATAATTCTGCGGGACCA' \
       'TGGTCGTCTCCTAACCTCAGGGTGGGATTCCTGGCAGGTGGACCGGGCGCGCATCGAGAGCATTCGGGGTTCCTACCAGCCAGGGAAATCGGGTCGACCACTAGGCAA' \
       'TGAGCGGCTCACACCGATTTTCTTAAGAGACGTAACAAAGCCCGCATTAACGGCTGGAGTGAATCACCGTACGACTACCTAAGCCTCATTGGGATCCACTGTAAACCC' \
       'CTTCGCCGGTGTTGGGTGTCCGCAACGCCTCTGCTTTTTGCGTACAGTCGGCGTGGTGGAGTCCGCGGCCATACTGGCGGTTGGTTTGTAGAACAGTGTAACGACGTG' \
       'TGTCACTGCCCCCCGTAGCTTCTATTGCCCTGTTTGGGAGGTTCTATAGGGGTTACAGAGTAGTTTTAAGTTTTAGCACGACAGCACCAGTATTGCCAGTGACGCCGT' \
       'TGAGGCCGCAAAAGTGATTAACCCCCGTGGGACCGGATACGTTCCCAGCGGCAATCCTTGTCTTACCGCCGGACTGCGGAGCGAAGGGAGAAGTAACCGTGGTAATTA'

print(dna)  # All on one line 

gistfile1.txt

dna = """ACGACGGATACGCGGGAGCTATTCATCTGTGTTGAGAAACACCGGAGAACTTATTGGTCTGTCAAGATTGCGACTGTGGTATAGCTCACCCGGTCGCGGCTTTCTAGT' \
       'TAGTGGCCAGCTCCCGTGTATTTGGAAGCTGAGAGAAGGACCCCTGTGGTTCGAATCAGCTCACGAGCGCTGGCACACCGCAATCAGCCGGCTAATAAAATTCGTACG' \
       'GACTGCCCCACACAAGAAGACGGTAAATTTATCAACACTATAGTTGCTATACACCAGGAGCGAGCGTAAATTTGTAGCGGTCAGATTAACTTGCTGGGAACGAACCAT' \
       'TGTCGCCCTCTGCAGCAAGTTAGTTGGCATCATTGGTACTGCCCTTCACTGGTAGCAGCTCCCCCTGTAATATATCCGTGGCCACTATTCAAGGGCTCAAATAGGCGA' \
       'CCCAGAGACCATTATAGGCGGTACAGCGCTGGTAGGTTTGCCTGGGCAGATATCGTTAGCCCCTTCTGCGCGCTATAAGATAGCGAAGGATAATTCTGCGGGACCA' \
       'TGGTCGTCTCCTAACCTCAGGGTGGGATTCCTGGCAGGTGGACCGGGCGCGCATCGAGAGCATTCGGGGTTCCTACCAGCCAGGGAAATCGGGTCGACCACTAGGCAA' \
       'TGAGCGGCTCACACCGATTTTCTTAAGAGACGTAACAAAGCCCGCATTAACGGCTGGAGTGAATCACCGTACGACTACCTAAGCCTCATTGGGATCCACTGTAAACCC' \
       'CTTCGCCGGTGTTGGGTGTCCGCAACGCCTCTGCTTTTTGCGTACAGTCGGCGTGGTGGAGTCCGCGGCCATACTGGCGGTTGGTTTGTAGAACAGTGTAACGACGTG' \
       'TGTCACTGCCCCCCGTAGCTTCTATTGCCCTGTTTGGGAGGTTCTATAGGGGTTACAGAGTAGTTTTAAGTTTTAGCACGACAGCACCAGTATTGCCAGTGACGCCGT' \
       'TGAGGCCGCAAAAGTGATTAACCCCCGTGGGACCGGATACGTTCCCAGCGGCAATCCTTGTCTTACCGCCGGACTGCGGAGCGAAGGGAGAAGTAACCGTGGTAATTA'

links and notes.txt

Sources: 

DNA structure & image; https://www.nature.com/scitable/topicpage/discovery-of-dna-structure-and-function-watson-397/
Generate random DNA sequences http://bioinformatics.org/sms2/random_dna.html
https://en.wikipedia.org/wiki/Start_codon
General DNA info https://www.coursera.org/learn/dna-decoded
Learning Bioinformatics - solving biology problems with programming: https://www.coursera.org/learn/bioinformatics 
Python bioinformatics problems: http://rosalind.info

reverse_dna.py

def other_strand(dna):
    dna_other_strand = ''
    for base in dna:  # making more general variable names in a function
        if base == 'A':
            # it's pair is a T
            dna_other_strand = dna_other_strand + 'T'
        elif base == 'T':
            dna_other_strand = dna_other_strand + 'A'
        elif base == 'C':
            dna_other_strand = dna_other_strand + 'G'
        elif base == 'G':
            dna_other_strand = dna_other_strand + 'C'
    return dna_other_strand


dna1 = 'ACCAGTACCAGTGT'   # how can you make the other side?
#       TGGTCATGGTCACA    # output

# A pairs with T   and     T pairs with A
# C pairs with G   and     G pairs with C
dna2 = 'GTACACCAGGTCTA'

print(other_strand(dna1))
print(other_strand(dna2))