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NetDNA[1.0].py

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+#!/usr/bin/python -w
+
+####Importing Libraries and python modules####
+import streamlit as st
+import pandas as pd
+import altair as alt
+from PIL import Image
+from Bio.Seq import Seq
+
+###Creating a Page title, logo and information about the web application###
+Picture  = Image.open('DNA.jpeg')
+
+####Displaying and Extending the image along the column width###
+st.image(Picture, use_column_width=True)
+
+###Writing a header about the web program###
+st.write("""
+***
+
+# NetDNA-1.0
+
+This is a web-based tool that uses the query DNA sequence to generate basic biological data:
+\n- Length of the Sequence
+\n- Count of Non-bases(if any)
+\n- Nucleotide Base-Count & its visualization
+\n- GC Content(%)
+\n- Melting Temperature(Tm)
+\n- Reverse Complement
+\n- Transcribed Sequence
+\n- Translated Sequence
+
+***
+""")
+
+###Creating a Text-box to get user input###
+
+#Header for the input sequence
+st.header("Please enter your DNA sequence:")
+
+user_input = ''
+DNA_Sequence = st.text_area("Input", user_input, height = 275)
+st.write("**Note**: Entering a Non-DNA sequence might display wrong results from step-7 (Results section)")
+
+st.write("""
+***
+""")
+
+###Converting the data to Upper case###
+DNA_Sequence = DNA_Sequence.upper()
+st.header("This is your DNA sequence:")
+DNA_Sequence
+
+st.write("""
+***
+""")
+###Removing All White Spaces###
+DNA_Sequence = ''.join(DNA_Sequence.split())
+
+###Displaying the Results###
+st.header("--**RESULTS**--")
+
+#Displaying the length of the given DNA Sequence
+length_DNA = len(DNA_Sequence)
+st.subheader("[1] Length of the given DNA sequence: ")
+st.write(length_DNA," bases")
+
+st.write("""
+***
+""")
+
+###Counting Non-bases in the sequence###
+Base_Count = (DNA_Sequence.count('A') + DNA_Sequence.count('T') + DNA_Sequence.count('G') + DNA_Sequence.count('C'))
+Non_Bases = (length_DNA - Base_Count)
+
+#Displaying the count of Non-bases
+st.subheader("[2] Number of Non-Bases in the given DNA Sequence: ")
+st.write(Non_Bases, " Non bases")
+
+st.write("""
+***
+""")
+
+#Displaying the Nucleotide Base Count in the given DNA Sequence
+st.subheader("[3] Nucleotide Base Count of the given DNA Sequence:")
+st.write("- Number of Adenine(A):", DNA_Sequence.count('A'))
+st.write("- Number of Thymine(T):", DNA_Sequence.count('T'))
+st.write("- Number of Guanine(G):", DNA_Sequence.count('G'))
+st.write("- Number of Cytosine(C):", DNA_Sequence.count('C'))
+
+st.write("""
+***
+""")
+
+###Creating a dataframe of the Nucleotide base count for Graphical visualization###
+data = {
+        'Nucleotide Base':  ['A', 'T', 'G', 'C'],
+        'Count': [DNA_Sequence.count('A'), DNA_Sequence.count('T'), DNA_Sequence.count('G'), DNA_Sequence.count('C')]
+        }
+df = pd.DataFrame (data, columns = ['Nucleotide Base','Count'])
+
+
+###Graphical Representation of the base count###
+st.subheader("[4] Graphical Representation of the Nucleotide Base count")
+Graph = alt.Chart(df).mark_bar().encode(x = 'Nucleotide Base', y = 'Count')
+
+#Adjusting the size of the bars in the Graph
+Graph = Graph.properties(width = alt.Step(75))
+
+#Displaying the Graph
+st.write(Graph)
+
+st.write("""
+***
+""")
+
+###GC Content of the given DNA Sequence###
+C_count = DNA_Sequence.count('C') ####Counting Cytosine###
+G_count = DNA_Sequence.count('G') ####Counting Guanine###
+
+try:
+    GC_content = (C_count+G_count)/length_DNA*100
+except:
+    GC_content = 0
+
+st.subheader("[5] GC content of the given DNA Sequence")
+st.write("-The GC content in the given DNA Sequence: %5.2f%%" % GC_content)
+
+st.write("""
+***
+""")
+
+###Melting Temperature(Tm)###
+st.subheader("[6] Melting Temperature (Tm)")
+if (length_DNA<14):
+      try:
+          Tm_less = (DNA_Sequence.count('A') + DNA_Sequence.count('T'))*2 + (DNA_Sequence.count('C') + DNA_Sequence.count('G')) * 4
+      except:
+          Tm_less = 0
+      st.write("-The Melting Temperature(Tm) of the given DNA sequence:", Tm_less, "°C")
+else:
+      try:
+          Tm_more = 64.9 +41*(DNA_Sequence.count('G')+DNA_Sequence.count('C')-16.4)/(DNA_Sequence.count('A')+DNA_Sequence.count('T')+DNA_Sequence.count('G')+DNA_Sequence.count('C'))
+      except:
+          Tm_more = 0
+      st.write("-The Melting Temperature(Tm) of the given DNA sequence:", Tm_more,"°C")
+
+st.write("""
+***
+""")
+
+###Reverse Complement of the given DNA Sequence###
+DNA_Sequence = Seq(DNA_Sequence)
+
+st.subheader("[7] Reverse Complement of the given DNA Sequence")
+st.write(DNA_Sequence.reverse_complement())
+
+st.write("""
+***
+""")
+
+###Transcribed Sequence of the given data###
+st.subheader("[8] Transcribed Sequence (DNA -> RNA)")
+st.write(DNA_Sequence.transcribe())
+
+st.write("""
+***
+""")
+
+###Translated Sequence of the given data###
+st.subheader("[9] Translated Sequence (RNA -> Protein)")
+st.write(DNA_Sequence.translate())
+
+st.write("""
+***
+""")
+
+###Displaying the Amino acid codes###
+AA_Code  = Image.open('AA-Codes.jpeg')
+st.image(AA_Code, use_column_width=True)
+st.write("(* or asterisk) = 'Stop codon' or 'Termination codon' ")
+###END###