Project: Introduction to Python for Life Sciences

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Kernel: Python 2 (SageMath)

Lists

Lets make a list:
Execute the code by pressing ctrl + enter
- Name: my_list
- Value: []

In [1]:

# Write here your code to make an empty list
my_list = []

In [2]:

print "'"

print '"'

'
"

Write your code to make lists:

empty list which can hold 4 items
list called molecules containing elements: DNA, RNA, Protein and Lipid
containing 4 sequences
containing at least 1 string, 1 integer, and 1 boolean

In [9]:

# Write here your code to make lists
my_list = [None]*4
molecules = ["DNA","RNA","Protein","Lipid","DNA"]
seqs = ["ATCG"]*4
mixed_list = ["ABC",3,True]

# Print the results
print(my_list)
print(molecules)
print(seqs)
print(mixed_list)

[None, None, None, None]
['DNA', 'RNA', 'Protein', 'Lipid', 'DNA']
['ATCG', 'ATCG', 'ATCG', 'ATCG']
['ABC', 3, True]
0

In [10]:

print molecules[1:].index("DNA")
print molecules[1:2].index("DNA")

3

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-10-20b0201bec85> in <module>()
      1 print molecules[1:].index("DNA")
----> 2 print molecules[1:2].index("DNA")

ValueError: 'DNA' is not in list

Accessing Lists

Using the lists that you have created, check what is stored at index 1 of the list 'molecules'

In [22]:

# molecules[1]?
print molecules[1]
# What is the index for 'DNA' in the list molecules?
print molecules[0]
# Try command list.index(object)
print molecules.index("DNA")

RNA
DNA
0

Lists – Exercise

Create the following 3 string variables with their restriction sites:
- eco_r1 : gaattc
- bam_h1 : ggatcc
- hind3 : aagctt
Make a list called restriction_enzymes containing the 3 restriction sites.
Using a single command print the restriction sites in the list on 3 different lines.
Print the first letter of eco_r1 using the list.

In [2]:

# Q1, hint: eco_r1 = ? 
# bam_h1 = ?
# hind3 = ?
eco_r1 = "gaattc"
bam_h1 = "ggatcc"
hind3 = "aagctt"

# Q2, hint: restriction_enzymes = 
restriction_enzymes = [eco_r1,bam_h1,hind3]

In [7]:

# Q3, hint: print "EcoRI: ", restriction_enzymes[?], ... 
print "EcoRI:",restriction_enzymes[0],"\n","BamH1:",restriction_enzymes[1],"\n","Hind3:",restriction_enzymes[2],"\n"

# OR use a for loop
for restrict in restriction_enzymes:
    print restrict

print " "

# OR be fancy and use join
print '\n'.join(restriction_enzymes)

print " "

EcoRI: gaattc 
BamH1: ggatcc 
Hind3: aagctt 

gaattc
ggatcc
aagctt
 
gaattc
ggatcc
aagctt
 

In [0]:

# Q4, hint: restriction_enzymes??
print restriction_enzymes
print restriction_enzymes[0][0]

In [13]:

restriction_enzymes = [eco_r1,bam_h1,hind3]

# Bonus question: Change first letter of eco_r1 restriction site from g to G using list 'restriction_enzymes'
restriction_enzymes[0] = restriction_enzymes[0][0].upper()+restriction_enzymes[0][1:]
print restriction_enzymes
#print restriction_enzymes[0][0]

restriction_enzymes[0] = restriction_enzymes[0].upper()
print restriction_enzymes

#restriction_enzymes[0][0] = restriction_enzymes[0][0].upper()
#Doesn't work You cant edit strings like this

['Gaattc', 'ggatcc', 'aagctt']
['GAATTC', 'ggatcc', 'aagctt']

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-13-59eeb8ac5c35> in <module>()
      9 print restriction_enzymes
     10 
---> 11 restriction_enzymes[0][0] = restriction_enzymes[0][0].upper()

TypeError: 'str' object does not support item assignment

Basic List operations

Adding (concatenate) two lists

Repeating items in list

Compare two lists: cmp(L1, L2)

Length of a list: len(L1)

Maximum value: max(L1)

Minimum value: min(L1)

In [24]:

# Try some list operations
my_list = [1, 2, 5] + [3, 4, 6]
my_list2 = [1, 2, 5] + [2, 4, "ZZZ"]
print my_list
print [3]*5
print " "
print cmp(my_list, my_list)
print cmp(my_list[1:], my_list)
print cmp(my_list, my_list[2:])

print " "
print cmp(my_list, my_list)
print " "

print len(my_list)
print max(my_list)
print min(my_list)

print len(my_list2)
print max(my_list2)
print min(my_list2)

[1, 2, 5, 3, 4, 6]
[3, 3, 3, 3, 3]
 
0
1
-1
 
0
 
6
6
1
6
ZZZ
1

Basic List operations - Exercise

Remember that we made a list of restriction enzymes as: restriction_enzymes = [eco_r1, bam_h1, hind3]. Create a new variable my_enzyme = 'catgac’
Make a new list with my_enzyme added to the existing list of restriction enzymes.
Make a new list containing 3 repetitions of eco_r1, 4 repetitions of bam_h1, and 2 repetitions of hind3.
What is the length of the lists you just created?
What is the maximum value of the list?
What is the minimum value of the list?

In [22]:

restriction_enzymes = [eco_r1,bam_h1,hind3]

# Create variable my_enzyme and concatenate it with restriction_enzyme list
my_enzyme = "actgcac"

print restriction_enzymes

restriction_enzymes.append(my_enzyme)
print restriction_enzymes

restriction_enzymes += [my_enzyme]
print restriction_enzymes

restriction_enzymes += my_enzyme
print restriction_enzymes

restriction_enzymes = restriction_enzymes + my_enzyme
# Create list with repeated entries and find its length

['gaattc', 'ggatcc', 'aagctt']
['gaattc', 'ggatcc', 'aagctt', 'actgcac']
['gaattc', 'ggatcc', 'aagctt', 'actgcac', 'actgcac']
['gaattc', 'ggatcc', 'aagctt', 'actgcac', 'actgcac', 'a', 'c', 't', 'g', 'c', 'a', 'c']

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-22-573ede14846e> in <module>()
     15 print restriction_enzymes
     16 
---> 17 restriction_enzymes = restriction_enzymes + my_enzyme
     18 # Create list with repeated entries and find its length
TypeError: can only concatenate list (not "str") to list

Looping Lists - Exercise

Calculate the number of nucleotides (A, T, G, and C) used by each restriction enzyme?
Calculate the total number of nucleotides used by all restriction enzymes taken together?
Use the list entry seqs given in the worksheet. How many DNA and RNA sequences are given in seqs? (Hint: try for loop, if elif conditions and string find command)
Remember EcoRI cuts at restriction site 'gaattc'. Can you check how many sequences given in list seqs have EcoRI motif?
Bonus Question: Make a list containing ['A', 'AA', 'AAA', 'AAAA', ….., 20 A].

In [0]:

In [11]:

eco_r1 = "gaattc"
bam_h1 = "ggatcc"
hind3 = "aagctt"
restriction_enzymes = [eco_r1.upper(), bam_h1.upper(), hind3.upper()]

# First try
for item in restriction_enzymes:
    print item

# range is a function that returns a list containing arithmetic progressions
range(10)

# If we need only the index
for index in range(len(restriction_enzymes)):
    print index

# If we need both the index and the item
for index, item in enumerate(restriction_enzymes):
    print index, item    

# Q1
# Calculate number of nucleotides using for loop


total_count = 0
for enzyme in restriction_enzymes:
    print enzyme
    count = enzyme.count("A") +  enzyme.count("T") + enzyme.count("C") + enzyme.count("G")
    count = len(enzyme)
    print count
    total_count += count

GAATTC
GGATCC
AAGCTT
0
1
2
0 GAATTC
1 GGATCC
2 AAGCTT
GAATTC
6
GGATCC
6
AAGCTT
6
0 20
20

In [19]:

# Q3
# Hint: try for loop, if elif conditions and string find command
seqs = ['actgactgactgaattcgactg','caucgaucgcgauacacgaucagcuacg','augcagacgacguacgu','atcgatcgatcgatcacgt','atcgtagctactagctagc','acgatcgtagctacgta','cgaucagucgaucgauccagcga','cguacguagcacaugcagucaguauacguacggacgacgac','catgactgactgatcgatgctgactgactg','atcggatctgaactgactg','actgactgactgactg','caucgaucgcgauacacgaucagcuacg','augcagacgacguacgu','atcgatcgaattcgatcgatcacgt','atcgtagctactagctagc','acgatcgaattcgtagctacgta','cgaucagucgaucgauccagcga','cguacguagcacaugcagucaguauacguacggacgacgac','catgactgactgatcgatgaattcgctgactgactg','aucggauccgaaccgacag']

for index,item in enumerate(seqs):
    seqs[index] = item.upper()
    
dna_count = 0
rna_count = 0
for seq in seqs:
    print(seq)
    print(seq.find('U'))
    if seq.find('U') != -1:
        rna_count += 1
    elif seq.find('G') != -1:
        dna_count += 1
        
print "-----------"
print dna_count, rna_count
print "-----------"

# Q4
# Hint: try for loop and append list
cut_seqs=0
cut_sequences = []
for seq in seqs:
    if seq.find(eco_r1.upper()) != -1:
        cut_seqs += 1
        #print seq
        cut_sequences.append(seq)
print(cut_sequences)

print(cut_seqs)
print(len(cut_sequences))

ACTGACTGACTGAATTCGACTG
-1
CAUCGAUCGCGAUACACGAUCAGCUACG
2
AUGCAGACGACGUACGU
1
ATCGATCGATCGATCACGT
-1
ATCGTAGCTACTAGCTAGC
-1
ACGATCGTAGCTACGTA
-1
CGAUCAGUCGAUCGAUCCAGCGA
3
CGUACGUAGCACAUGCAGUCAGUAUACGUACGGACGACGAC
2
CATGACTGACTGATCGATGCTGACTGACTG
-1
ATCGGATCTGAACTGACTG
-1
ACTGACTGACTGACTG
-1
CAUCGAUCGCGAUACACGAUCAGCUACG
2
AUGCAGACGACGUACGU
1
ATCGATCGAATTCGATCGATCACGT
-1
ATCGTAGCTACTAGCTAGC
-1
ACGATCGAATTCGTAGCTACGTA
-1
CGAUCAGUCGAUCGAUCCAGCGA
3
CGUACGUAGCACAUGCAGUCAGUAUACGUACGGACGACGAC
2
CATGACTGACTGATCGATGAATTCGCTGACTGACTG
-1
AUCGGAUCCGAACCGACAG
1
-----------
11 9
-----------
['ACTGACTGACTGAATTCGACTG', 'ATCGATCGAATTCGATCGATCACGT', 'ACGATCGAATTCGTAGCTACGTA', 'CATGACTGACTGATCGATGAATTCGCTGACTGACTG']
4
4

Modifying Lists

Take list seqs and add 3 random DNA/RNA sequences at the end of the list
Take list seqs and add 'atcg' as the third sequence of the list
Create a new sorted list seq_sort from seqs

In [0]:

# Try modifying lists
molecules[?] = ?
print molecules

# Use list functions

In [16]:

list1 = [2,1,3,4]
list2 = list1

print list1
print list2

list1.sort()

print list1
print list2

[2, 1, 3, 4]
[2, 1, 3, 4]
[1, 2, 3, 4]
[2, 1, 3, 4]

Modifying Lists

Remove 'atcg' sequence of the list seqs
Print 5th to 10th sequence entry from the lists seqs and seq_sort

In [0]:

# Use list functions

Converting strings to Lists

Two essential command of list conversion are:

Create a list from a string: StringName.split()
Create a string from lists: ' '.join(ListName)

Split 'atgcatgcatgc' sequence using split() command
Create a list by splitting 'atgcatgcatgc' sequence using 't' as the separator.

In [28]:

# Try split and join command
amino = 'Ala Cys Phe Val Glu'.split(" ")
a = ''.join(amino)
print a
print list(a)

# Try split command

AlaCysPheValGlu
['A', 'l', 'a', 'C', 'y', 's', 'P', 'h', 'e', 'V', 'a', 'l', 'G', 'l', 'u']

Tuples

Tuples are Python sequence but unlike lists they are immutable. Tuples use parentheses and lists use square brackets.

tup1 = ('physics', 'chemistry', 1997, 2000)

tup2 = (1, 2, 3, 4, 5 )

tup3 = ('a', 'b', 'c', 'd')

Accessing tuples:

print "tup1[0]: ", tup1[0]

print "tup2[1:5]: ", tup2[1:5]

Try to assign tuples:

tup1[2] = 2015

tup4 = tup2 + tup3

In [0]:

# Make tuples with different items

# Access different elements from tuples

# Assign different values to tuples

Tuples Exercise

Suppose you want to find distance between Carbon atoms in a protein sequence.

Assign 4 tuples each containing the 3D co-ordinates:

	X	Y	Z
C29	0.55	1.256	-1.153
C103	1.28	-1.72	1.24
C115	1.59	1.73	1.04
C118	1.36	-1.86	-1.74

Calculate square distance between different carbon atoms. Hint use: (x1-x2)^2+(y1-y2)^2+(z1-z2)^2

In [22]:

# Hint: make a list
# Each element of the list can contain a tuples with coordinates of a carbon atom
=(0.55,1.256,-1.153)
c103=(1.28,-1.72,1.24)
c115=(1.59,1.73,1.04)
c118=(1.36,-1.86,-1.74)
c_atoms = [c29,c103,c115,c118]

# use two for loops to calculate distance between their X, Y and Z

for i in range(len(c_atoms)):
    for j in range(i,len(c_atoms)):
        # Option 1, prior knowledge
        x1,y1,z1=c_atoms[i]
        x2,y2,z2=c_atoms[j]
        
        distance = (x1-x2)**2+(y1-y2)**2+(z1-z2)**2
        print i,j, distance
        
        # Option 2, fewer assumptions
        distance = 0
        #for x in range(len(c_atoms[i])):
        #    distance += (c_atoms[i][x]-c_atoms[j][x])**2
        #print i,j, distance

0 0.0
1 15.115925
2 6.115525
3 10.710125
1 0.0
2 12.0386
3 8.9064
2 0.0
3 20.6694
3 0.0

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