Since the ProtParam module takes the protein sequence as a string you have to call str() on a Seq object to return the full sequence as a string.

This is a bit tricky, because you often don't actually have to do this conversion explicitly, because Python does this automatically with a print statement. If you are using Biopython 1.44 or older, using str(record.seq) will give just a truncated representation. Instead use record.seq.tostring() which is still available in the current Biopython releases for backwards compatibility.

For example:

from Bio import SeqIO
from Bio.SeqUtils import ProtParam

handle = open("example.fasta") 
for record in SeqIO.parse(handle, "fasta"): 
    seq = str(record.seq)
    X = ProtParam.ProteinAnalysis(seq)
    print X.count_amino_acids() 
    print X.get_amino_acids_percent() 
    print X.molecular_weight() 
    print X.aromaticity() 
    print X.instability_index() 
    print X.flexibility() 
    print X.isoelectric_point() 
    print X.secondary_structure_fraction()

Thank you so very much for your help. It worked...:)

Thanks Best regards, Saba