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###################### | ||
# Import libraries | ||
###################### | ||
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import pandas as pd | ||
import streamlit as st | ||
import altair as alt | ||
from PIL import Image | ||
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###################### | ||
# Page Title | ||
###################### | ||
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image = Image.open('dna-logo.jpg') | ||
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st.image(image, use_column_width=True) | ||
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st.write(""" | ||
# DNA Nucleotide Count Web App | ||
This app counts the nucleotide composition of query DNA! | ||
*** | ||
""") | ||
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###################### | ||
# Input Text Box | ||
###################### | ||
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#st.sidebar.header('Enter DNA sequence') | ||
st.header('Enter DNA sequence') | ||
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sequence_input = ">DNA Query 2\nGAACACGTGGAGGCAAACAGGAAGGTGAAGAAGAACTTATCCTATCAGGACGGAAGGTCCTGTGCTCGGG\nATCTTCCAGACGTCGCGACTCTAAATTGCCCCCTCTGAGGTCAAGGAACACAAGATGGTTTTGGAAATGC\nTGAACCCGATACATTATAACATCACCAGCATCGTGCCTGAAGCCATGCCTGCTGCCACCATGCCAGTCCT" | ||
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#sequence = st.sidebar.text_area("Sequence input", sequence_input, height=250) | ||
sequence = st.text_area("Sequence input", sequence_input, height=250) | ||
sequence = sequence.splitlines() | ||
sequence = sequence[1:] # Skips the sequence name (first line) | ||
sequence = ''.join(sequence) # Concatenates list to string | ||
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st.write(""" | ||
*** | ||
""") | ||
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## Prints the input DNA sequence | ||
st.header('INPUT (DNA Query)') | ||
sequence | ||
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## DNA nucleotide count | ||
st.header('OUTPUT (DNA Nucleotide Count)') | ||
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### 1. Print dictionary | ||
st.subheader('1. Print dictionary') | ||
def DNA_nucleotide_count(seq): | ||
d = dict([ | ||
('A',seq.count('A')), | ||
('T',seq.count('T')), | ||
('G',seq.count('G')), | ||
('C',seq.count('C')) | ||
]) | ||
return d | ||
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X = DNA_nucleotide_count(sequence) | ||
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#X_label = list(X) | ||
#X_values = list(X.values()) | ||
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X | ||
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### 2. Print text | ||
st.subheader('2. Print text') | ||
st.write('There are ' + str(X['A']) + ' adenine (A)') | ||
st.write('There are ' + str(X['T']) + ' thymine (T)') | ||
st.write('There are ' + str(X['G']) + ' guanine (G)') | ||
st.write('There are ' + str(X['C']) + ' cytosine (C)') | ||
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### 3. Display DataFrame | ||
st.subheader('3. Display DataFrame') | ||
df = pd.DataFrame.from_dict(X, orient='index') | ||
df = df.rename({0: 'count'}, axis='columns') | ||
df.reset_index(inplace=True) | ||
df = df.rename(columns = {'index':'nucleotide'}) | ||
st.write(df) | ||
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### 4. Display Bar Chart using Altair | ||
st.subheader('4. Display Bar chart') | ||
p = alt.Chart(df).mark_bar().encode( | ||
x='nucleotide', | ||
y='count' | ||
) | ||
p = p.properties( | ||
width=alt.Step(80) # controls width of bar. | ||
) | ||
st.write(p) |