Python_03_problemset

Python_03_problemset

1. Write a script that calculates the AT content of the DNA string found below. AT content is the 
proportion of bases that are either A or T. You will need to use some mathmatical functions as well 
as a python function. It is ALWAYS a good idea to test your code with test data. For example, the 
below sequence is long and you don't know for sure how many As and Ts are present. Test your codee 
with a DNA string that you KNOW the correct answer. In AATTGGCCA you know you have 3 As and 2 Ts.

GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATTCGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCG


#!/usr/bin/env python3

dna = GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATTCGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCG

length=len(dna)






#!/usr/bin/env python3

#GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGG$


dna =
'ATGCTGAAA'

length=len(dna)

string= "this sequence: {} is {} nucleotides long"
string.format(dna, length)
print(string.format(dna, length))

pfb14:files admin$ nano myscript_6.py
pfb14:files admin$ python3 myscript_6.py 
  File "myscript_6.py", line 6
    dna = 
         ^
SyntaxError: invalid syntax



#!/usr/bin/env python3

dna = 'ATGCTGAAA'

length=len(dna)

string= "this sequence: {} is {} nucleotides long"
string.format(dna, length)
print(string.format(dna, length))

pfb14:files admin$ python3 myscript_6.py 
this sequence: ATGCTGAAA is 9 nucleotides long


pfb14:files admin$ nano myscript_6.py

#!/usr/bin/env python3

dna = 'GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCT$

length = len(dna)

string1 = "this sequence: {} is {} nucleotides long"

string1.format(dna, length)

print(string1.format (dna, length) )


Tcount = dna.count('T')
Acount = dna.count('A')

ATcontent = ((Tcount + Acount)/length *100 )

string2 = "the AT content is {} %"

string2.format(ATcontent)

print(string2.format (ATcontent) )

pfb14:files admin$ python3 myscript_6.py 
this sequence: GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATTCGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCG is 842 nucleotides long
the AT content is 42.042755344418055 %

2.

Now add in lines of code to calculate GC content of the above DNA string. Run with test data first!!



#!/usr/bin/env python3


dna = 'GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCC$


length = len(dna)

string1 = "this sequence: {} is {} nucleotides long"

string1.format(dna, length)

print(string1.format (dna, length) )


Tcount = dna.count('T')
Acount = dna.count('A')

ATcontent = ((Tcount + Acount)/length *100 )

string2 = "the AT content is {} %"

string2.format(ATcontent)

print(string2.format (ATcontent) )


Gcount = dna.count('G')
Ccount = dna.count('C')

GCcontent = ((Gcount + Ccount)/length *100 )

string3 = "the GC content is {} %"

string3.format(GCcontent)

print(string3.format (GCcontent) )


pfb14:files admin$ python3 myscript_6.py 
this sequence: GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATTCGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCG is 842 nucleotides long
the AT content is 42.042755344418055 %
the GC content is 57.95724465558195 %


3. 

Write a new script that prints out the reverse complement of the above DNA string.

pfb14:files admin$ nano myscript_7.py

#!/usr/bin/env python3

dna = 'GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCC$

dnaT= dna.replace('T', 'a')
dnaTA=dnaT.replace('A', 't')
dnaTAG=dnaTA.replace('G', 'c')
dnaTAGC=dnaTAG.replace('C', 'g')

print(dnaTAGC)

pfb14:files admin$ python3 myscript_7.py 
ctaccctaaccccaaaaggggagggtacacgagttctgaccgcgattttcaaaactcgaagagttttcagatctcggtggcaggtccctcgtccatcgacgacccgaggcccctgtgaaacgcaagcccgaccctcgcacgaaaggtgctgccactgtgcgaagggacctaaccgtcggtctgacggaaggcccagtgacggtacctcctcggcgtcagtctaggatcgcagctcgggggagactcagtcctttgtaaaagtctggatacctttgatgaaggacttttgttgcaagacagggggaacggcagggttcgttacctactaaactacgacaggggcctgctataacttgttaccaagtgacttctgggtccaggtctacttcgagggtcttaagcggtctccgacgaggggggcaccggggacgtggtcgtcgaggatgtggccgccggggacgtggtcgggggaggaccggggacagtagaagacagggaagggtcttttggatggtcccgtcgatgccaaaggcagacccgaagaacgtaagaccctgtcggttcagacactgaacgtgcatgaggggacgggagttgttctacaaaacggttgaccggttctggacgggacacgtcgacacccaactaaggtgtgggggcgggccgtgggcgcaggcgcggtaccggtagatgttcgtcagtgtcgtgtactgcctccaacactccgcgacgggggtggtactcgcgacgagtctatcgctaccagaccggggaggagtcgtagaataggctcaccttcctttaaacgcacacctcataaacctactgtctttgtgaaaagc





**** this only did the reverse. question asked for the reverse complement!!



#!/usr/bin/env python3

dna = 'GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCC$

dnaT= dna.replace('T', 'a')
dnaTA=dnaT.replace('A', 't')
dnaTAG=dnaTA.replace('G', 'c')
dnaTAGC=dnaTAG.replace('C', 'g')

print(dnaTAGC[::-1])

pfb14:files admin$ python3 myscript_7.py 
cgaaaagtgtttctgtcatccaaatactccacacgcaaatttccttccactcggataagatgctgaggaggggccagaccatcgctatctgagcagcgctcatggtgggggcagcgcctcacaacctccgtcatgtgctgtgactgcttgtagatggccatggcgcggacgcgggtgccgggcgggggtgtggaatcaacccacagctgcacagggcaggtcttggccagttggcaaaacatcttgttgagggcaggggagtacgtgcaagtcacagacttggctgtcccagaatgcaagaagcccagacggaaaccgtagctgccctggtaggttttctgggaagggacagaagatgacaggggccaggagggggctggtgcaggggccgccggtgtaggagctgctggtgcaggggccacggggggagcagcctctggcgaattctgggagcttcatctggacctgggtcttcagtgaaccattgttcaatatcgtccggggacagcatcaaatcatccattgcttgggacggcaagggggacagaacgttgttttcaggaagtagtttccataggtctgaaaatgtttcctgactcagagggggctcgacgctaggatctgactgcggctcctccatggcagtgacccggaaggcagtctggctgccaatccagggaagcgtgtcaccgtcgtggaaagcacgctcccagcccgaacgcaaagtgtccccggagcccagcagctacctgctccctggacggtggctctagacttttgagaagctcaaaacttttagcgccagtcttgagcacatgggaggggaaaaccccaatcccatc


5.

Write a script to find the start position of an EcoRI in the above sequence. Remember DNA sequences start with a 1 and a python string starts with a 0. Run with test data first.

pfb14:files admin$ nano myscript_8.py

#!/usr/bin/env python3

dna = 'GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCC$

print( dna.find('GAATTC') + 1)

pfb14:files admin$ python3 myscript_8.py
396


6.  What is the location in the DNA string of the EcoR1 cut site? Calculate the first and last nucleotides of each restriction fragment.

location of the EcoR1 cut site is one base pair over

based on python numbering, it should cut at position 396
based on DNA bp counting, it should cut at position 397

EcoRI will generate 2 restriction fragments (sequence GAATTC)

Fragment 1:

start nucleotide = G
end nucleotide = G

Fragment 2: 

start nucleotide = A
end nucleotide = G


7. 

Extract the the restricion fragments. Print each fragment along with its postion in the whole DNA sequence and its length. Use string formating to format your print statemnt.

#!/usr/bin/env python3

dna = 'GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGAC$

print('fragment 1')

fragment1= dna[0:396]   
position1= dna.find(fragment1)
length1= len(dna[0:396])

print("{}\t{}\t{}".format(fragment1, position1 +1, length1) )

print ('fragment 2')

fragment2= dna[396:]   
position2= dna.find(fragment2)
length2= len(dna[396:])

print("{}\t{}\t{}".format(fragment2, position2 +1, length2) )

pfb14:files admin$ python3 myscript_8.py
fragment 1
GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAG	1	396
fragment 2
AATTCGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCG	397	446



8, 9, and 10

Create a list and add each fragment to it.

Sort the list.

Sort the list by fragment length. Check out documentation of the key argument.

#!/usr/bin/env python3
#Python_03_question9

dna = 'GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGAC$

#fragment 1

fragment1= dna[0:396]
position1= dna.find(fragment1)
length1= len(dna[0:396])

#fragment 2

fragment2= dna[396:]
position2= dna.find(fragment2)
length2= len(dna[396:])

ecoRI_frags = [fragment1, fragment2]

print(ecoRI_frags)

print(length1, length2)

print(sorted (ecoRI_frags, key=len) )


pfb14:files admin$ python3 myscript_9.py
['GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAG', 'AATTCGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCG']
396 446
['GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAG', 'AATTCGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCG']





>>> help(sorted)

Help on built-in function sorted in module builtins:

sorted(iterable, /, *, key=None, reverse=False)
    Return a new list containing all items from the iterable in ascending order.
    
    A custom key function can be supplied to customize the sort order, and the
    reverse flag can be set to request the result in descending order.
 
11.

Interogate the difference between these two ways to copy a list. Both are not correct.

alter the lists after the "copy" by adding a new element to the list
print the lists before and after you alter the "copy"


>>> my_list = ['a', 'bb', 'ccc']
>>> list_copy = my_list
>>> list_copy.append('blah')
>>> list_copy()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: 'list' object is not callable
>>> print(list_copy)
['a', 'bb', 'ccc', 'blah']
>>> print (my_list)
['a', 'bb', 'ccc', 'blah'

****this way created another name for the original list - didn't actually copy

>>> my_list = ['a', 'bb', 'ccc']
>>> list_copy = my_list.copy()
>>> list_copy.append('blah')
>>> print(list_copy)
['a', 'bb', 'ccc', 'blah']
>>> print(my_list)
['a', 'bb', 'ccc']

****this way created a copy of my_list and made additions to the copy.