first commit

app.py

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+#from turtle import shape
+import streamlit as st
+#from st_keyup import st_keyup
+import pandas as pd
+import numpy as np
+from st_aggrid import AgGrid, GridOptionsBuilder,GridUpdateMode,DataReturnMode
+
+import os
+
+cwd=os.getcwd()+'/'+'data/'
+
+#get genes list
+listA = pd.read_csv(cwd+"20200513_library_1_2_unbalanced_dJR051.csv",index_col=False)
+listB = pd.read_csv(cwd+"20200513_library_3_4_unbalanced_dJR052.csv",index_col=False)
+listC = pd.read_csv(cwd+"20200513_library_5_6_unbalanced_dJR053.csv",index_col=False)
+#variants=listA['sgID_A'].unique()
+variants=listA['gene'].unique()
+variants_s=sorted(variants)
+
+#Also read LR guides
+listA_found_ref = pd.read_csv(cwd+"seta_found_ref1.csv",index_col=False)
+listA_notfound_ref = pd.read_csv(cwd+"seta_notfound_ref1.csv",index_col=False)
+
+listA_found_lr = pd.read_csv(cwd+"seta_found_LR1.csv",index_col=False)
+listA_notfound_lr = pd.read_csv(cwd+"seta_notfound_LR1.csv",index_col=False)
+
+
+
+
+st.title('Long Read Guides Search')
+#st.markdown('**Please select an option from the sidebar**')
+
+#st.write(variants)
+
+Calc = st.sidebar.radio(
+    "",
+    ('ReadME', 'Tools Selection Menu'))
+
+
+if Calc == 'ReadME':
+    #st.markdown("[Introduction](#Introduction)")    
+    #st.markdown("[How do base editors work](#How-do-base-editors-work)")
+    
+    expander = st.expander("How to use this app")   
+else:
+#if Calc == 'Selection Menu':
+    #ReadMe = st.sidebar.checkbox('ReadME',value=False)
+    select_variant = st.sidebar.selectbox(
+        "Please select variant",
+        variants_s
+    )
+    #ref_sgrna=listA[listA['sgID_A']==select_variant][['protospacer_A','protospacer_B']]
+    ref_listA=listA[listA['gene']==select_variant][['guide_type','protospacer_A','protospacer_B','sgID_AB']]
+    #ref_listA=listA[listA['gene']==select_variant]
+    #st.write(ref_listA)
+    
+    ref_listB=listB[listB['gene']==select_variant][['guide_type','protospacer_A','protospacer_B','sgID_AB']]
+    #st.write(ref_listB)
+    
+    
+    ref_listC=listC[listC['gene']==select_variant][['guide_type','protospacer_A','protospacer_B','sgID_AB']]
+    #st.write(ref_listC)
+    #m=pd.merge(ref_listA,ref_listC,ref_listC)
+    listA_concatenated_orig = pd.concat([ref_listA,ref_listB,ref_listC])
+
+    
+    st.write('Original Guides (all 6 from 3 sets)')
+    st.write(listA_concatenated_orig)
+    
+    st.write('GRCh38 SetA Guides Found with at most 2 Missmatches')
+    a_ref=ref_listA.sgID_AB.values[0].split('|')
+    #check GRCh38
+    seta_found0_ref=listA_found_ref[listA_found_ref['gene']==a_ref[0]]
+    seta_found1_ref=listA_found_ref[listA_found_ref['gene']==a_ref[1]]
+    listA_concatenated_found_ref = pd.concat([seta_found0_ref,seta_found1_ref])
+    st.write(listA_concatenated_found_ref)
+
+    st.write('LR SetA Guides Found with at most 2 Missmatches')
+    seta_found0_lr=listA_found_lr[listA_found_lr['gene']==a_ref[0]]
+    seta_found1_lr=listA_found_lr[listA_found_lr['gene']==a_ref[1]]
+    listA_concatenated_found_LR = pd.concat([seta_found0_lr,seta_found1_lr])
+    st.write(listA_concatenated_found_LR)
+
+    st.write('GRCh38 SetA Guides Not Found')
+    seta_notfound0_ref=listA_notfound_ref[listA_notfound_ref['gene']==a_ref[0]]
+    seta_notfound1_ref=listA_notfound_ref[listA_notfound_ref['gene']==a_ref[1]]
+    listA_concatenated_notfound_ref = pd.concat([seta_notfound0_ref,seta_notfound1_ref])
+    st.write(listA_concatenated_notfound_ref)
+    
+    st.write('LR SetA Guides Not Found')
+    seta_notfound0_lr=listA_notfound_lr[listA_notfound_lr['gene']==a_ref[0]]
+    seta_notfound1_lr=listA_notfound_lr[listA_notfound_lr['gene']==a_ref[1]]
+    listA_concatenated_notfound_lr = pd.concat([seta_notfound0_lr,seta_notfound1_lr])
+    st.write(listA_concatenated_notfound_lr)
+    
+    
+    #protospacer_A

data/header.csv

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+gene,ref_guide,chr,position,mutated_guide,strnad,num_mismatch

data/header1.csv

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+gene,ref_guide

requirements.txt

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+streamlit
+pandas
+numpy
+streamlit-nested-layout
+streamlit-on-Hover-tabs
+streamlit-aggrid
+streamlit-drawable-canvas