Question

USE Python 2.7(screen shot code with indentation and output exactly in the question) the task is: takes in a list of protein sequences as input and finds all the transmembrane domains and returns them in a list for each sequence in the list with given nonpolar regions and returns the lists for those.

1. This code should call two other functions that you write: regionProteinFind takes in a protein sequence and should return a list of 10 amino acid windows, if the sequence is less than 10 amino acids, it should just return that sequence. (initially it should grab amino acids 1-10…the next time it is called it should grab amino acids 2-11…) for each sequence in the list. testcode: "protein='MKLVVRPWAGCWWSTLGPRGSLSPLGICPLLMLLWATLR'' the regionProteinFind returns:['MKLVVRPWAG','KLVVRPWAGC','LVVRPWAGCW','VVRPWAGCWW','VRPWAGCWWS','RPWAGCWWST','PWAGCWWSTL','WAGCWWSTLG','AGCWWSTLGP','GCWWSTLGPR', 'CWWSTLGPRG','WWSTLGPRGS','WSTLGPRGSL','STLGPRGSLS','TLGPRGSLSP','LGPRGSLSPL','GPRGSLSPLG','PRGSLSPLGI','RGSLSPLGIC','GSLSPLGICP','SLSPLGICPL','LSPLGICPLL','SPLGICPLLM','PLGICPLLML','LGICPLLMLL','GICPLLMLLW','ICPLLMLLWA','CPLLMLLWAT','PLLMLLWATL','LLMLLWATLR'] 2nd testcode; protein=MP region protein sequence should return: ['ME']

2. A second function called testForTM , which should calculate and return the decimal fraction of ten amino acid window which are nonpolar for each sequence in the list. the nonpolar regions are (A,V,L,I,P,M,F,W). my code for this is:

def testForTM(AAWindow):

totalNP= 0

nonPolarList=['A', 'V', 'L', 'I', 'P', 'M', 'F', 'W']

for aa in AAWindow:

if aa in nonPolarList:

totalNP+=1

return totalNP/10.0 #THIS SHOULD DEVIDE BY len(AAWindow) so it works for sequences less than 10 length like 'MP'

3. The last function,tmSCANNER should call the get protein region and test for TM and Ultimately, as a result the code should be used to scan each protein sequence in the list as input generating list of numbers of non polar for each protein sequence which measures the fraction of nonpolar residues in each 10bp window(it slides 10 amino acids at a time until it is at the last aa window of a protein sequence with any length and give the lists for those. The code should output what is displayed below.

#Test code for TMFinder

listOfProtein=['MKLVVRPWAGCWWSTLGPRGSLSPLGICPLLMLLWATLR', 'MARKCSVPLVMAWLTWTTSRAPLPH', 'MPWPTSITXXXXXXSWSPEWLSSGLRSILGWEQPRVSHKGHSHEWHRRP'] tmValuesList=TMFinder(listOfProtein) print 'The list of TM values are:', tmValuesList as a result it should print out this list: ["protein 1:'MKLVVRPWAGCWWSTLGPRGSLSPLGICPLLMLLWATLR'", 'TMValue:[0.7, 0.6, 0.7, 0.7, 0.6, 0.5, 0.6, 0.5, 0.5, 0.4, 0.4, 0.4, 0.4, 0.3, 0.4, 0.5, 0.4, 0.5, 0.4, 0.5, 0.6, 0.7, 0.7, 0.8, 0.8, 0.8, 0.9, 0.8, 0.9, 0.8]',"protein2:'MARKCSVPLVMAWLTWTTSRAPLPH'", 'TMValue:[0.6, 0.6, 0.6, 0.7, 0.8, 0.8, 0.9, 0.8, 0.7, 0.6, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5]',"protein3:'MPWPTSITXXXXXXSWSPEWLSSGLRSILGWEQPRVSHKGHSHEWHRRP'",'TMValue:[0.5, 0.4, 0.3, 0.2, 0.1, 0.1, 0.2, 0.1, 0.2, 0.2, 0.3, 0.4, 0.4, 0.4, 0.4, 0.5, 0.4, 0.4, 0.4, 0.5, 0.4, 0.4, 0.4, 0.4, 0.5, 0.4, 0.5, 0.5, 0.4, 0.3, 0.3, 0.2, 0.2, 0.2, 0.1, 0.2, 0.1, 0.1, 0.1]']

Thank you for the help!!!

Answer 1

ANSWER:

• I have provided properly commented code in both text and image format so it will be easy for you to copy the code as well as check for proper indentation.
• I have provided the output image of code so you can easily cross check the correct output of the code.
• Have a nice and healthy day!!

CODE TEXT

## function regionProteinFind to find all AAWindoe
def regionProteinFind(protein):
## if protein length is less than 10 return protein itself in list
if len(protein)<10:
return [protein]
## otherwise we use list comprehension to form list of all
## window of length 10
## range(n) creates a list of whole numbers from 0 to n-1
return [protein[i:i+10] for i in range(len(protein)+1-10)]

## function testForTM
def testForTM(AAWindow):
totalNP= 0
nonPolarList=['A', 'V', 'L', 'I', 'P', 'M', 'F', 'W']
for aa in AAWindow:
if aa in nonPolarList:
totalNP+=1
return totalNP/float(len(AAWindow))

## function TM Finder
def TMFinder(listOfProtein):
## creating a empty list
output_list=[]
## iterating through each protein in listOfProtein
## using enumerate to fetch index of protein in the list
for index,protein in enumerate(listOfProtein):
## appending formated string containing protein number and protein
## as asked in format
output_list.append("Protein{}:'{}'".format(index+1,protein))
## fetching list of protein windows by calling regionProteinFind
prot_wind=regionProteinFind(protein)
## using list comprehension to find TM value of each window
tm_list=[testForTM(window) for window in prot_wind]
## apeninding TMValue in output_list in the format asked
output_list.append('TMValue:{}'.format(tm_list))
## returning output_list
return output_list

## defining input
listOfProtein=['MKLVVRPWAGCWWSTLGPRGSLSPLGICPLLMLLWATLR', 'MARKCSVPLVMAWLTWTTSRAPLPH', 'MPWPTSITXXXXXXSWSPEWLSSGLRSILGWEQPRVSHKGHSHEWHRRP']
## calling TMFinder and priniting output
print TMFinder(listOfProtein)

CODE IMAGE

OUTPUT IMAGE