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:","nn",Gravity) #Hydrophobicty Calculation by using kd scale print("n","Hydrophobicity:","nn",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:","nn",aa_composition) #Volume Calculation by using quantiprot library vol = get_aa2volume(analysed_seq) print("n","Volume of amino acids in protein:","nn",str(vol))
The features are:
- Computed volume
- Relative surface accessibility (RSA)
- Secondary structure (SS)
I have calculated volume, Hydrophobicity, and SS but I don't know how can I merge them in one matrix?
plz help me