Upload app.py

app.py

@@ -0,0 +1,191 @@
+from Bio.Blast import NCBIWWW, NCBIXML
+from Bio.Seq import Seq
+from Bio import SeqIO
+from Bio.SeqUtils import GC
+import time
+import warnings
+import streamlit as st
+from PIL import Image
+from io import StringIO
+
+img = Image.open("image.png")
+
+st.image(img, use_column_width=True)
+
+st.write(""" ## **Your results will display here :**
+""")
+def set_button_style():
+    button_style = """
+        <style>
+            .stButton button {
+                background-color: #FF6F61;
+                color: white;
+                border-radius: 100px;
+                border: 2px solid #FFFFFF; 
+                box-shadow: 2px 2px 5px #000000;
+                width: 160px;
+            }
+        </style>
+    """
+    st.markdown(button_style, unsafe_allow_html=True)
+
+    
+st.sidebar.title('Protein alignment with BLAST')
+
+up = st.sidebar.file_uploader("Choose an existing fasta file", accept_multiple_files=False)
+if up :
+    fasta = up.read()
+
+
+seq = st.sidebar.text_area('Or enter a sequence to analyze : ')
+
+b1 = st.sidebar.button("Calculate GC")
+b2 = st.sidebar.button("Replicate")
+b3 = st.sidebar.button("Transcribe")
+b4 = st.sidebar.button("Back-Transcribe")
+b5 = st.sidebar.button("Translate")
+
+type = st.sidebar.text_input('Enter BLAST type : ',placeholder='exemple : blastp, blastn ...')
+data = st.sidebar.text_input('Enter the database : ', placeholder='exemple : nt, nr ...')
+detailed = st.sidebar.text_input('Enter detailed search : ', placeholder='Homo sapiens')
+set_button_style()
+b = st.sidebar.button("Run BLAST")
+s = st.sidebar.button("Run detailed search")
+
+
+
+def blast(seq, type, data):
+
+    st.write("""Starting BLAST search...""") 
+    start_time = time.time()
+    result_handle2 = NCBIWWW.qblast(type, data, seq)
+    end_time = time.time()
+    
+    st.write("""BLAST search completed.""")
+    st.write(f"Time taken: {end_time - start_time:.2f} seconds.")
+    
+    with open("output.xml", "w") as out_handle:
+        out_handle.write(result_handle2.read())
+    st.write("Results saved to output.xml")
+    st.write("===================================")
+    result_handle = open("output.xml")
+    blast_record = NCBIXML.read(result_handle)
+    st.write(""" **Results :** """)
+    count = 0
+    for alignment in blast_record.alignments:
+        st.write("**"+str(alignment.title)+"**")
+        for hsp in alignment.hsps:
+            st.write(str(hsp.query[0:50]))
+            st.write(str(hsp.query[0:50]))
+            st.write(str(hsp.query[0:50]))
+            percentage_result = (hsp.query_end - hsp.query_start + 1) / hsp.align_length * 100
+            st.write(str(hsp))
+            if percentage_result >= 50:  
+                st.write(f'<p style="color:green;">{percentage_result:.2f}</p>', unsafe_allow_html=True)
+            else:
+                st.write(f'<p style="color:red;">{percentage_result:.2f}</p>', unsafe_allow_html=True)
+        count += 1
+        if count == 10:
+            break
+
+def detailed_search(detailed):
+    
+    result_handle = open("output.xml")
+    blast_record = NCBIXML.read(result_handle)
+    
+    st.write(" Detailed search on : " + "**" + str(detailed) + "**")
+    for alignment in blast_record.alignments:
+        if detailed in alignment.title:
+            st.write(str(alignment.title))
+            for hsp in alignment.hsps:
+                st.write(str(hsp.query[0:50]))
+                st.write(str(hsp.match[0:50]))
+                st.write(str(hsp.sbjct[0:50]))
+                st.write(str(hsp.positives) + str(hsp.score) + str(hsp.expect) + str(hsp.bits) + str(hsp.gaps))
+
+def save_seq(seq):
+    with open("sequenceinput.fsa", "w") as file:
+        file.write(str(seq))
+    st.write("sequence saved to sequenceinput.fsa")
+
+if seq :
+    save_seq(seq)
+
+if (seq and  type  and data and b)  :
+    blast(seq, type, data)
+elif (up and type and data and b) :
+    blast(fasta, type, data)
+ 
+if detailed and s : 
+    detailed_search(detailed)
+
+
+def calculate(seq):
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")  # Ignore all warnings
+        gc_content = GC(seq)
+    st.write(f"### **GC :** {gc_content}")
+
+if seq and b1 :
+    calculate(seq)
+elif up and b1 :
+    calculate(fasta.decode())
+
+def reverse(seq):
+    sequence = Seq(seq)
+    r_seq = sequence.reverse_complement()
+    chunked_r_seq = [r_seq[i:i+50] for i in range(0, len(r_seq), 50)]
+
+    st.write("### **Reversed sequence :**")
+    for chunk in chunked_r_seq:
+        st.write("#### " + str(chunk))
+
+if seq and b2 :
+    reverse(seq)
+elif up and b2 : 
+    reverse(fasta)
+
+def transcribe_seq(seq):
+    sequence = Seq(seq)
+    r_seq = sequence.transcribe()
+    chunked_r_seq = [r_seq[i:i+50] for i in range(0, len(r_seq), 50)]
+
+    st.write("### **Transcribed sequence :** ")
+    for chunk in chunked_r_seq:
+        st.write("#### " + str(chunk))
+
+if seq and b3 :
+    transcribe_seq(seq)
+elif up and b3 :
+    transcribe_seq(fasta)
+
+def back_transcribe_seq(seq):
+    sequence = Seq(seq)
+    r_seq = sequence.back_transcribe()
+    chunked_r_seq = [r_seq[i:i+50] for i in range(0, len(r_seq), 50)]
+
+    st.write("### **Back-Transcribed sequence :** ")
+    for chunk in chunked_r_seq:
+        st.write("#### " + str(chunk))
+
+if seq and b4 :
+    back_transcribe_seq(seq)
+elif up and b4 :
+    back_transcribe_seq(fasta)
+
+def translate_seq(seq):
+    try :
+        sequence = Seq(seq)
+        r_seq = sequence.translate()
+        chunked_r_seq = [r_seq[i:i+50] for i in range(0, len(r_seq), 50)]
+
+        st.write("### **Translated sequence :** ")    
+        for chunk in chunked_r_seq:
+            st.write("#### " + str(chunk))
+    except Exception as e:
+        st.write(f"#### Unable to translate this sequence! {e}")
+
+if seq and b5 :
+    translate_seq(seq)
+elif up and b5 : 
+    transcribe_seq(fasta)