python_script4.py

#!/usr/bin/env python3

#import modules we have had examples on so far
import sys
import math

dna = GATGGGATTGGGGTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATTCGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCG

#counts A and T content
at_content = dna.count('T') + dna.count('A')

#counts C and G contentcut = ecor1_end_site = ecor1_start_site + 5ecor1_cut_site = 2cut = ecor1_end_site = ecor1_start_site + 5ecor1_cut_site = 2 
cg_content = dna.count('C') + dna.count('G')

#complement ATGC sequence in dna by sequential replacing USING CASE AS A DINSTINGUISHER--use loop later.
compA = dna.replace('A', 't')
compAT = compA.replace('T', 'a')
compATG = compAT.replace('G', 'c')
compATGC = compATG.replace('C', 'g')

dna_complement = compATGC.upper()

#reversing a string [begin:end:step] is extended slice syntax. Leaving begin and end off and specifying a step of -1, it reverses a string

dna_reverse_complement = dna_complement[::-1]

#EcoR1 recognition start and site report. EcoR1 = 5' GAATTC 3'

ecor1 = "GAATTC"
ecor1_start_site = 1 + int(dna.find("GAATTC")) #using this as the fragment generator will proper slice the stirngs at the restriction location
ecor1_cut_site = 1 + ecor1_start_site
ecor1_end_site = ecor1_start_site + 5

#extract restriction fragments annd print with tab delimeter
ecor1_frag1 = dna[0:ecor1_start_site]
ecor1_frag2 = dna[ecor1_start_site:]

#formating output of above scripts to print out a string with given indexes
#and is tab separated
ecor1_print = '''The Ecor1 restriction locations and product are:
{0}\t{1}\t{2}\t{3}.'''

print(ecor1_print.format(0, ecor1_frag1, ecor1_cut_site, ecor1_frag2))

#add the restriction fragments to a list

ecor1_fragments_list = [ecor1,str(ecor1_start_site), str(ecor1_end_site)]


#put EcoR1 restriction fragments into a list and sort.

frag_list = [ecor1_frag1, ecor1_frag2]
frag_list.sort()