cleanup

app.py

@@ -1,5 +1,5 @@
 import streamlit as st
-from tiger import tiger_predict, TARGET_LEN, NUCLEOTIDE_TOKENS
+from tiger import tiger_exhibit, TARGET_LEN, NUCLEOTIDE_TOKENS
 
 
 @st.cache
@@ -23,9 +23,9 @@ if len(st.session_state['userInput']) < TARGET_LEN:
 
 # valid input
 elif all([True if nt.upper() in NUCLEOTIDE_TOKENS.keys() else False for nt in st.session_state['userInput']]):
-    predictions = tiger_predict(st.session_state['userInput'])
-    st.write('Model predictions: ', predictions)
-    csv = convert_df(predictions)
+    on_target_predictions, off_target_predictions = tiger_exhibit(st.session_state['userInput'])
+    st.write('Model predictions: ', on_target_predictions)
+    csv = convert_df(on_target_predictions)
     st.download_button(label='Download CSV file', data=csv, file_name='tiger_predictions.csv', mime='text/csv')
 
 # invalid input

tiger.py

@@ -65,7 +65,7 @@ def process_data(transcript_seq: str):
     return target_seq, guide_seq, model_inputs
 
 
-def tiger_predict(transcript_seq: str):
+def predict_on_target(transcript_seq: str):
 
     # load model
     if os.path.exists('model'):
@@ -132,16 +132,21 @@ def find_off_targets(guides, batch_size=1000):
     return df_off_targets
 
 
-if __name__ == '__main__':
+def tiger_exhibit(transcript):
 
-    # simple test case
-    transcript_sequence = 'ATGCAGGACGCGGAGAACGTGGCGGTGCCCGAGGCGGCCGAGGAGCGCGC'.lower()  # first 50 from EIF3B-003's CDS
-    sorted_predictions = tiger_predict(transcript_sequence)
+    # on-target predictions
+    on_target_predictions = predict_on_target(transcript)
 
-    # report top guides only
-    sorted_predictions = sorted_predictions.iloc[:NUM_TOP_GUIDES]
-    print(sorted_predictions)
+    # keep only top guides
+    on_target_predictions = on_target_predictions.iloc[:NUM_TOP_GUIDES]
 
     # scan for off-targets for top guides
-    off_targets = find_off_targets(sorted_predictions.index.values.tolist())
-    print(off_targets)
+    off_targets = find_off_targets(on_target_predictions.index.values.tolist())
+
+    return on_target_predictions, off_targets
+
+
+if __name__ == '__main__':
+
+    # simple test case
+    print(tiger_exhibit('ATGCAGGACGCGGAGAACGTGGCGGTGCCCGAGGCGGCCGAGGAGCGCGC'.lower()))  # first 50 from EIF3B-003's CDS