Giving error while uploading fasta file

🎈 Using Streamlit
1

import streamlit as st
import neatbio.sequtils as utils
from Bio.Seq import Seq
from Bio import SeqIO
from collections import Counter
import io

data pkgs

import matplotlib.pyplot as plt
import matplotlib
matplotlib.use(“Agg”)
import numpy as np
st.set_option(‘deprecation.showfileUploaderEncoding’, False)

def main():

st.title('Simple Bioinformatics App')
menu = ["DNA Sequence","Dot Plot"]
choice = st.sidebar.selectbox("Select Activity",menu)



if choice == "DNA Sequence":
    st.subheader("DNA Sequence Analysis")
    seq_file = st.file_uploader("Upload FASTA File",type = ["fasta","fa"])
    # assume bytes_io is a `BytesIO` object
    byte_str = seq_file.read()

    #Convert to a "unicode" string object
    text_io = byte_str.decode('UTF-8')  # Or use the encoding you expect

    # convert to io.StringIO, which I think SeqIO will understand well.
    SeqIO.read(io.StringIO(text_obj))
    #text_io = io.TextIOWrapper(seq_file)




    if seq_file is not None:
        dna_record = SeqIO.read(seq_file,"fasta")
        #st.write(dna_record)
        dna_seq = dna_record.seq
        desc = dna_record.description
        details = st.radio("Details", ("Description", "Sequence"))
        if details == "Description":
             st.write(desc)
        elif details == "Sequence":
             st.write(dna_seq)

        # Nucleotide Frequencies
        st.subheader("Nucleotide Frequencies")
        dna_freq = Counter(dna_seq)
        st.write(dna_freq)
        adenine_color = st.beta_color_picker("Adenine Color")
        guanine_color = st.beta_color_picker("Guanine Color")
        thymine_color = st.beta_color_picker("Thymine Color")
        cytosil_color = st.beta_color_picker("Cytosil Color")



        if st.button("Plot Freq"):
            barlist = plt.bar(dna_freq.keys(), dna_freq.values())
            barlist[0].set_color(adenine_color)
            barlist[1].set_color(thymine_color)
            barlist[2].set_color(guanine_color)
            barlist[3].set_color(cytosil_color)

            st.pyplot()


        st.subheader("DNA Composition")
        gc_score = utils.gc_content(str(dna_seq))
        at_score = utils.at_content(str(dna_seq))
        st.json({"GC Content ":gc_score, "AT Content ":at_score})

        # Nucleotide Count
        nt_count = st.text_input("Enter Nucleotide Here","Type Nucleotide Alphabet")
        st.write("Number of {} nucleotide is : {} ".format((nt_count),str(dna_seq).count(nt_count)))

        # Protein Synthesis
        p1 = dna_seq.translate()
        aa_freq = Counter(str(p1))

        st.subheader("Protein Synthesis")
        if st.checkbox("Transcription"):
            st.write(dna_seq.transcribe())
        elif st.checkbox("Translation"):
            st.write(dna_seq.translate())
        elif st.checkbox("Complement"):
            st.write(dna_seq.complement())
        elif st.checkbox("AA Frequency"):
            st.write(aa_freq)
        elif st.checkbox("AA Plot Frequency"):
            #aa_color = st.beta_color_picker("Amino Acid Color")
            #barlist = plt.bar(aa_freq.keys(), aa_freq.values(), color = aa_color)
            plt.bar(aa_freq.keys(), aa_freq.values())
            #barlist[0].set_color(aa_color)
            st.pyplot()
        elif st.checkbox("Full Amino Acid Name"):
            aa_name = str(p1).replace("*","")
            st.write(aa_name)
            st.write("--------------------------")
            st.write(utils.convert_1to3(aa_name))



elif choice == "Dot Plot":
    st.subheader("Generate Dot Plot For Two Sequences")
    seq_file = st.file_uploader("Upload 1st FASTA File", type=["fasta", "fa"])
    seq_file2 = st.file_uploader("Upload 2nd FASTA File", type=["fasta", "fa"])

    # text_io = io.TextIOWrapper(seq_file)

    if seq_file and seq_file2 is not None:
        dna_record1 = SeqIO.read(seq_file, "fasta")
        dna_record2 = SeqIO.read(seq_file2, "fasta")

        # st.write(dna_record)
        dna_seq1 = dna_record1.seq
        dna_seq2 = dna_record2.seq

        desc1 = dna_record1.description
        desc2 = dna_record2.description

        details = st.radio("Details", ("Description", "Sequence"))
        if details == "Description":
            st.write(desc1)
            st.write("----------")
            st.write(desc2)
        elif details == "Sequence":
            st.write(dna_seq1)
            st.write("----------")
            st.write(dna_seq2)

        custom_limit = st.number_input("Select max number of Nucleotide ",10,200,25)
        if st.button("Dot Plot"):
            st.write("Comparing the first {} Nucleotide of Two Sequences ".format(custom_limit))
            dotplotx(dna_seq1[0:custom_limit], dna_seq2[0:custom_limit])
            st.pyplot()

def delta(x,y):
return 0 if x == y else 1

def M(seq1,seq2,i,j,k):
return sum(delta(x,y) for x,y in zip(seq1[i:i+k], seq2[j:j+k]))

def makeMatrix(seq1,seq2,k):
n = len(seq1)
m = len(seq2)
return [[M(seq1,seq2,i,j,k) for j in range(m-k+1)] for i in range(n-k+1)]

def plotMatrix(M, t, seq1, seq2, nonblank = chr(0x25A0), blank = ’ ‘):
print(’ |’ + seq2)
print(’-’*(2 + len(seq2)))
for label,row in zip(seq1, M):
line = ‘’.join(nonblank if s < t else blank for s in row)
print(label + ‘|’ + line )

def dotplot(seq1, seq2, k=1, t=1):
M = makeMatrix(seq1,seq2,k)
plotMatrix(M,t,seq1,seq2)

# Convert to Fxn

def dotplotx(seq1,seq2):
plt.imshow(np.array(makeMatrix(seq1,seq2,1)))
# on x axis list all sequnces of seq2
xt = plt.xticks(np.arange(len(list(seq2))), list(seq2))
# on y axis list all sequnces of seq1
yt = plt.yticks(np.arange(len(list(seq1))), list(seq1))
plt.show()

if name == ‘main’:
main()