Update app.py

app.py

@@ -56,6 +56,8 @@ with st.form('get signature'):
     if glob.glob(os.path.join(os.path.dirname(SigProfilerMatrixGenerator.__file__),'references/chromosomes/tsb/GRCh37/')+'*txt') == []:
         st.write('There is no reference genome, we need to download this')
         refdownload=True
+    else:
+        refdownload=False    
     file_to_lookat=st.file_uploader('VCF upload here',type=[".vcf"],accept_multiple_files=True)
     remove_old_vcf()
     sub=st.form_submit_button('submit input')
@@ -66,13 +68,14 @@ if sub and file_to_lookat !=[]:
     dirtest=os.path.join(os.path.dirname(SigProfilerMatrixGenerator.__file__),'references/chromosomes/tsb/GRCh37/')+'*txt'
     st.write(dirtest)
     #st.write(sys.path)
-    with st.spinner('downloading hg19 reference'):
-        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(dirtest)
-            for i in seev:
-                st.write(i)
+    if refdownload=True:
+        with st.spinner('downloading hg19 reference'):
+            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(dirtest)
+                for i in seev:
+                    st.write(i)
         ##genInstall.install('GRCh37')
 
     if not os.path.exists('input'):
@@ -93,7 +96,7 @@ if sub and file_to_lookat !=[]:
     #shutil.copy2(vcfuse,'input/'+vcfuse)
     #pdb.set_trace()
     with st.spinner('computing signatures'):
-        sig.sigProfilerExtractor("vcf", "output", "input", minimum_signatures=1, maximum_signatures=3)
+        sig.sigProfilerExtractor("vcf", "output", "input", minimum_signatures=1, maximum_signatures=3,nmf_test_conv= 1000,nmf_tolerance= 1e-    10,max_nmf_iterations=100000,min_nmf_iterations= 1000)
    
   #show_pdf('output/SBS96/Suggested_Solution/COSMIC_SBS96_Decomposed_Solution/SBS96_Decomposition_Plots.pdf')
     dl(file_to_lookat)