Getting error while upload

[arighosh1]

When I am uploading a fasta file it is showing that StreamModeError: Fasta files must be opened in text mode. Where is the problem I made?

[enesbasbug]

First of all, hello!

You can check this out, it may help https://github.com/streamlit/streamlit/issues/3057

arighosh1 @.***>, 8 Haz 2021 Sal, 17:45 tarihinde şunu yazdı:

When I am uploading a fasta file it is showing that StreamModeError: Fasta files must be opened in text mode. Where is the problem I made?

[image: image] https://user-images.githubusercontent.com/8570451/121206622-9fd90d00-c846-11eb-80d8-435c45980667.png

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[arighosh1]

I read the link, but I could not understand exactly where I need to put the code part. Can you please help?

On Tue, Jun 8, 2021 at 12:47 PM Enes Basbug @.***> wrote:

First of all, hello!

You can check this out, it may help https://github.com/streamlit/streamlit/issues/3057

arighosh1 @.***>, 8 Haz 2021 Sal, 17:45 tarihinde şunu yazdı:

When I am uploading a fasta file it is showing that StreamModeError: Fasta files must be opened in text mode. Where is the problem I made?

[image: image] < https://user-images.githubusercontent.com/8570451/121206622-9fd90d00-c846-11eb-80d8-435c45980667.png

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < https://github.com/enesbasbug/Bioinformatics-App-with-Streamlit/issues/1>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AKNF7R4MKQNGBPLITGE4WPDTRYUJXANCNFSM46KDXRBA

.

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-- Mr. Aritra Ghosh PhD Student Department of Computer Science & Electrical Engineering Florida Atlantic University Boca Raton, Florida, U.S.A 33486

[arighosh1]

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)

assume bytes_io is a BytesIO object

byte_str = seq_file.read()

Convert to a "unicode" string object

text_obj = 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))

if choice == "DNA Sequence":
    st.subheader("DNA Sequence Analysis")
    seq_file = st.file_uploader("Upload FASTA File",type = ["fasta","fa"])
    #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()

I am sure, I put the code part in wrong place

[arighosh1]

Please help me, sir. I am stuck