| 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") |
| 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) |
|
|
