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Python_03_problemset.md

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Python 3 Problem Set -- Strings

  1. What are considered sequences in Python?
  2. What is the length of the following DNA string? Is this DNA string a Python sequence?
GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATTCGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCG

  1. Make sure to commit your changes along the way. You can wait until the end to push them to your remote repo, if you like, or you can do it now. It is probably smart to commit after each problem set question.

  2. In the interpreter:

    • Create a variable named 'DNA' which contains the sequence above.
    • Count the number of A's
    • Count the number of T's
    • Count the number of G's
    • Count the number of C's

  3. In the interpreter:

    • Create a variable named 'bird' with the contents 'chicken'
    • convert the contents of 'bird' to be uppercase and print

  4. Create a script that counts the number of A's, T's, C's, and G's irregardless of case:

GATGGGATTggggttttccccTCCCATGTGCTCAAGACTGGCGCTaaaaGttttGAGCTTCTCaaaaGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCggggACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGccccCTCTGAGTCAGGAAACAttttCAGACCTATGGAAACTACTTCCTGaaaaCAACGTTCTGTccccCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTccccGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATTCGCCAGAGGCTGCTccccCCGTGGccccTGCACCAGCAGCTCCTACACCGGCGGccccTGCACCAGccccCTCCTGGccccTGTCATCTTCTGTCCCTTCCCAGaaaaCCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTccccTGCCCTCAACAAGATGttttGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACAccccCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGccccCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGccccTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACttttCG
  1. Find and replace all instances of 'T' with 'U' in this DNA sequence. Start with a small test sequence to make sure you are converting all the T's to U's.
GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATTCGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCG
  1. Now do the same find and replace in this sequence, notice the mixed cases. Start with a small test sequence with mixed cases to make sure you are getting the correct count.
GATGGGATTggggttttccccTCCCATGTGCTCAAGACTGGCGCTaaaaGttttGAGCTTCTCaaaaGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCggggACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGccccCTCTGAGTCAGGAAACAttttCAGACCTATGGAAACTACTTCCTGaaaaCAACGTTCTGTccccCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTccccGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATTCGCCAGAGGCTGCTccccCCGTGGccccTGCACCAGCAGCTCCTACACCGGCGGccccTGCACCAGccccCTCCTGGccccTGTCATCTTCTGTCCCTTCCCAGaaaaCCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTccccTGCCCTCAACAAGATGttttGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACAccccCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGccccCACCATGAGCGCT
  1. Write a script that calculates the AT content in this DNA string. 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 code with a DNA string that you KNOW the correct answer. In AATTGGCCA you know you have 3 As and 2 Ts.
    • Now add in lines of code to calculate GC content of the above DNA string. Run with test data first!!
GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATTCGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCG
  1. Extract and print the substring from nucleotide number 100 (not the same as its index) to nucleotide number 200 in this DNA sequence. Start with a small test sequence to make sure you are getting the correct substring.
GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATTCGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCG

  1. Count the number of G's in your substring

  2. Now use this DNA sequence and count the G's in your substring (100-200) but it should be irregardless of case:

GATGGGATTggggttttccccTCCCATGTGCTCAAGACTGGCGCTaaaaGttttGAGCTTCTCaaaaGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCggggACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGccccCTCTGAGTCAGGAAACAttttCAGACCTATGGAAACTACTTCCTGaaaaCAACGTTCTGTccccCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTccccGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATTCGCCAGAGGCTGCTccccCCGTGGccccTGCACCAGCAGCTCCTACACCGGCGGccccTGCACCAGccccCTCCTGGccccTGTCATCTTCTGTCCCTTCCCAGaaaaCCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTccccTGCCCTCAACAAGATGttttGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACAccccCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGccccCACCATGAGCGCT
  1. Write a new script that prints out the reverse complement of the above DNA string. Hint for reverse. Use string formating for printing.
 Original Sequence  5'ATGCAGGGGAAACATGATTCAGGAC 3'  
 Complement         3'TACGTCCCCTTTGTACTAAGTCCTG 5'  
 Reverse Complement 5'GTCCTGAATCATGTTTCCCCTGCAT 3'
  1. Write a script to find the starting nucleotide position of an EcoRI site in the below DNA sequence. Remember DNA sequences start with a 1 and a python string starts with a 0. Run with test data first.
GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATTCGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCG:

Also find the ending nucleotide position of the EcoRI site? Use string formating to print out these two values like this:

EcoRI startPos:yourStartPos endPos:yourEndPos
  1. ADD/COMMIT/PUSH