Delete App.py

App.py

@@ -1,71 +0,0 @@
-import streamlit as st
-import zipfile
-import urllib.request
-import glob
-import SigProfilerMatrixGenerator
-from SigProfilerMatrixGenerator import install as genInstall
-import shutil
-import os
-from SigProfilerExtractor import sigpro as sig
-import sys
-import base64
-import streamlit.components.v1 as components
-
-curdir= os.getcwd()
-
-def remove_old_vcf():
-    vcfrem=glob.glob('input/*.vcf')
-    for filepath in vcfrem:
-        os.remove(filepath)
-    vcfrem=glob.glob('input/input/*.vcf')    
-    for filepath in vcfrem:
-        os.remove(filepath)  
-
-def show_pdf(file_path):
-    with open(file_path,"rb") as f:
-        base64_pdf = base64.b64encode(f.read()).decode('utf-8')
-    pdf_display = f'<iframe src="data:application/pdf;base64,{base64_pdf}" width="1500" height="1000" type="application/pdf"></iframe>'
-    st.markdown(pdf_display, unsafe_allow_html=True)
-
-
-
-
-if st.button('get reference genome'):
-    st.write(os.path.dirname(SigProfilerMatrixGenerator.__file__))
-    dirtest=os.path.dirname(SigProfilerMatrixGenerator.__file__)
-    #st.write(sys.path)
-    urllib.request.urlretrieve('https://dl.dropboxusercontent.com/s/et97ewsct862x7m/references.zip?dl=0','references.zip')
-    with zipfile.ZipFile('references.zip', 'r') as zip_ref:
-        zip_ref.extractall(dirtest)
-        seev=glob.glob('/home/appuser/venv/lib/python3.9/site-packages/SigProfilerMatrixGenerator/references/*')
-        for i in seev:
-            st.write(i)
-    ##genInstall.install('GRCh37')
-
-if not os.path.exists('input'):
-    os.mkdir('input')
-
-if not os.path.exists('input/input'):
-    os.mkdir('input/input')
-
-file_to_lookat=st.file_uploader('VCF upload here',type=[".vcf"],accept_multiple_files=True)
-remove_old_vcf()
-
-if file_to_lookat !=[]:
-    bytes_data=file_to_lookat[0].read()
-    with open(os.path.join("input",file_to_lookat[0].name),"wb") as f:
-        f.write(bytes_data)
-        f.close()
-    
-    #vcfuse=glob.glob('file_to_lookat[0].name')[0]
-    #shutil.copy2(vcfuse,'input/'+vcfuse)
-    #pdb.set_trace()
-    with st.spinner('computing signatures'):
-        sig.sigProfilerExtractor("vcf", "output", "input", minimum_signatures=1, maximum_signatures=3)
-   
-    show_pdf('output/SBS96/Suggested_Solution/COSMIC_SBS96_Decomposed_Solution/SBS96_Decomposition_Plots.pdf')
-    
-    components.iframe("https://cancer.sanger.ac.uk/signatures/sbs/", height=3000,width=800)
-    show_pdf('output/ID83/Suggested_Solution/COSMIC_ID83_Decomposed_Solution/ID83_Decomposition_Plots.pdf')
-    components.iframe("https://cancer.sanger.ac.uk/signatures/id/",height=3000,width=800)
-    remove_old_vcf()