Create new file

app.py

@@ -0,0 +1,71 @@
+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()