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Python script to calculate properties of amino acids

I want to make a python script that can get as input sequence of N amino acids, and the output is a matrix of Nx6 containing 6 features about any of the acids.

I have developed this script :

#Importing Libraries
import numpy as np
import pandas as pd
from Bio.SeqUtils.ProtParam import ProteinAnalysis
from Bio.SeqUtils.ProtParam import ProtParamData
from quantiprot.metrics.aaindex import get_aa2volume, get_aa2hydropathy
from quantiprot.metrics.basic import average

#Input amino acid
 my_seq = input("Enter Your Sequence : ")
 SEQ = my_seq.upper()

#Analysis
analysed_seq = ProteinAnalysis(SEQ)
MW=  analysed_seq.molecular_weight()
Gravity = analysed_seq.gravy()
aa_composition = analysed_seq.count_amino_acids()
aa_percentage=analysed_seq.get_amino_acids_percent()
HP = analysed_seq.protein_scale(window=7, param_dict=ProtParamData.kd)
Sec_Str = analysed_seq.secondary_structure_fraction()

 #Amino Acid Compsoition Calculation
  print("\n" ,"AA count:",aa_composition,"\n")

  #Molecular Weight Calculation
   print("Molecular Weight : ",MW)


   #Gravity Calculation
    print("\n","Gravity:","\n\n",Gravity)
    #Hydrophobicty Calculation by using kd scale
    print("\n","Hydrophobicity:","\n\n",HP)
    #kd → Kyte & Doolittle Index of Hydrophobicity
   #Flex → Normalized average flexibility parameters (B-values)
   #hw → Hopp & Wood Index of Hydrophilicity
   #em → Emini Surface fractional probability

  #Amino Acid Percent Calculation

 print("\n","Percentage of Amino Acids in Protein:","\n\n",aa_composition)


 #Volume Calculation by using quantiprot library
 vol =  get_aa2volume(analysed_seq)
print("\n","Volume of amino acids in protein:","\n\n",str(vol))

The features are:

  1. Computed volume
  2. Hydrophobicity
  3. Polarity
  4. Relative surface accessibility (RSA)
  5. Secondary structure (SS)
  6. Type

I have calculated volume, Hydrophobicity, and SS but I don't know how can I merge them in one matrix?

Please help me

python
• 9,808 views • link
updated by Ram Ram • written by anasjamshed anasjamshed

Could you provide an example showing what do those six features look like? If they are all lists, you can easily stack them by numpy.vstack to a 2D array

• 0 views • link
written by Jianyu Jianyu

first, I have to calculate Polarity Relative surface accessibility (RSA) and Type but I am not sure which library I can use?

• 0 views • link
written by anasjamshed anasjamshed

Can anyone help me please?

• 0 views • link
written by anasjamshed anasjamshed

1 answer

To me this sounds like a data-presentation question. You could do some simple string manipulation to output the fields for each protein into a single tab-separated string, and then have each row separated by newline. Such a tab-separated file can be easily viewed nicely in Excel etc.

Something like this -

outputs=[] # put this code before beginning to analyze the sequences

# run this code for each of your N amino acids
features=vol+"\t"+HP+"\t"+....[your other features]...+"\n"
outputs.append(features) 

#Put this code after you are done with all the sequences - 
with open('output', 'w') as f:
    for i in range(len(outputs)):
    f.write(outputs[i])
• 0 views • link
written by c_u c_u

outputs.append()=HP ^ SyntaxError: cannot assign to function call

• 0 views • link
written by anasjamshed anasjamshed

Oh yes, it was about the use of append, I had made an error there. I have changed the code, hopefully it should work now

• 0 views • link
written by c_u c_u

i have tried this again:

outputs=[] 
#Analysis
analysed_seq = ProteinAnalysis(SEQ)
MW=  analysed_seq.molecular_weight()
Gravity = analysed_seq.gravy()
aa_composition = analysed_seq.count_amino_acids()
aa_percentage=analysed_seq.get_amino_acids_percent()
HP = analysed_seq.protein_scale(window=7, param_dict=ProtParamData.kd)
Sec_Str = analysed_seq.secondary_structure_fraction()
features=Sec_Str+"\t"+HP+"\t"+MW+"\n"
outputs.append(features)

but its giving me this error :

---> 22 features=Sec_Str+"\t"+HP+"\t"+MW+"\n"
     23 outputs.append(features)
     24 

TypeError: can only concatenate tuple (not "str") to tuple
• 0 views • link
written by anasjamshed anasjamshed

Well that means some the 3 items that you are concatenating are tuples, and some other items are strings. It might be best to convert everything to string. You should first figure out the type of each of the 3 items, and then convert the ones that are tuples into string. This is one way to do it

• 0 views • link
written by c_u c_u

Also, don't forget to upvote comments and answers that were helpful in any way. It is a way to show appreciation for the time that another person spent trying to help you :)

• 0 views • link
written by c_u c_u

i am trying this now:

#Importing Libraries
import numpy as np
import pandas as pd
from Bio.SeqUtils.ProtParam import ProteinAnalysis
from Bio.SeqUtils.ProtParam import ProtParamData
from quantiprot.metrics.aaindex import get_aa2volume, get_aa2hydropathy
from quantiprot.metrics.basic import average

#Input amino acid
my_seq = input("Enter Your Sequence : ")
SEQ = my_seq.upper()

outputs=[] 
#Analysis
analysed_seq = ProteinAnalysis(SEQ)
MW=  analysed_seq.molecular_weight()
Gravity = analysed_seq.gravy()
aa_composition = analysed_seq.count_amino_acids()
aa_percentage=analysed_seq.get_amino_acids_percent()
HP = analysed_seq.protein_scale(window=7, param_dict=ProtParamData.kd)
Sec_Str = analysed_seq.secondary_structure_fraction() #Volume Calculation by using quantiprot library
vol =  get_aa2volume(analysed_seq)
features="Composition:"+str(aa_composition)+" Hydrophobicity:"+str(HP)+" Volume:"+str(vol.mapping)+" Secondary Structure:"+str(Sec_Str)+" Molecular Weight:"+str(MW)
outputs.append(features) 

properties = np.array(outputs)
print(properties)

and it gives me this result:

Enter Your Sequence: ASDFMLL
["Composition:{'A': 1, 'C': 0, 'D': 1, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 2, 'M': 1, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 1, 'T': 0, 'V': 0, 'W': 0, 'Y': 0} Hydrophobicity:[1.4000000000000001] Volume:{'A': 1.0, 'C': 2.43, 'D': 2.78, 'E': 3.78, 'F': 5.89, 'G': 0.0, 'H': 4.66, 'I': 4.0, 'K': 4.77, 'L': 4.0, 'M': 4.43, 'N': 2.95, 'P': 2.72, 'Q': 3.95, 'R': 6.13, 'S': 1.6, 'T': 2.6, 'V': 3.0, 'W': 8.08, 'Y': 6.47} Secondary Structure:(0.42857142857142855, 0.14285714285714285, 0.5714285714285714) Molecular Weight:795.9429"]
• 0 views • link
written by anasjamshed anasjamshed

but now this script:

with open('output', 'w') as f:
    for i in len(outputs):
        f.write(outputs[i])

gives me an error:

---> 30     for i in len(outputs):
     31         f.write(outputs[i])

TypeError: 'int' object is not iterable
• 0 views • link
written by anasjamshed anasjamshed

One way to resolve that error is to replace for i in len(outputs): with for i in range(len(outputs)): so that it now becomes an iterable

• 0 views • link
written by c_u c_u

Please accept the answer if it was helpful. That encourages us to help you in the future as well.

• 0 views • link
written by c_u c_u

I want to calculate Polarity, Relative surface accessibility (RSA), and Type but I am not sure which library I can use?

• 0 views • link
written by anasjamshed anasjamshed

Well, since that is a separate issue, I would suggest that you should ask a new question for it, after accepting this answer.

• 0 views • link
written by c_u c_u

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