progress

app.py

@@ -64,7 +64,13 @@ def process_input():
             else:
                 st.session_state.transcripts = df
 
-    # TODO: convert to upper and check for ACGT only
+    # convert ot upper case as used by tokenizer
+    st.session_state.transcripts[tiger.SEQ_COL] = st.session_state.transcripts[tiger.SEQ_COL].apply(lambda s: s.upper())
+
+
+    # if src_seq and all([True if nt.upper() in NUCLEOTIDE_TOKENS.keys() else False for nt in src_seq]):
+    # elif src_seq is not None:
+    #     st.write('Invalid input!')
     print(st.session_state.transcripts)
 
 
@@ -131,18 +137,6 @@ if __name__ == '__main__':
                 check_off_targets=st.session_state.check_off_targets
             )
 
-    # # input-specific configuration
-    # if manual_mode:
-    #     src_seq = st.session_state['manual_seq']
-    #     status_text = manual_entry.empty()
-    #     status_bar = manual_entry.progress(0)
-    # elif fasta_mode:
-    #     src_seq = st.session_state['fasta_seq']
-    #     status_text = fasta_form.empty()
-    #     status_bar = fasta_form.progress(0)
-    # else:
-    #     src_seq = status_bar = status_text = None
-    #
     # # valid input
     # if src_seq and all([True if nt.upper() in NUCLEOTIDE_TOKENS.keys() else False for nt in src_seq]):
     #     on_target, off_target = tiger_exhibit(pd.DataFrame(dict(id=['ManualEntry'], seq=[src_seq])),
@@ -160,6 +154,3 @@ if __name__ == '__main__':
     #     elif option == 'On and Off Target' and len(off_target) == 0:
     #         st.write('We did not find any off-target effects!')
     #
-    # # invalid input
-    # elif src_seq is not None:
-    #     st.write('Invalid input!')

tiger.py

@@ -38,7 +38,7 @@ NUM_MISMATCHES = 3
 RUN_MODES = dict(
     all='All on-target guides per transcript',
     top_guides='Top {:d} guides per transcript'.format(NUM_TOP_GUIDES),
-    titration='Top {:d} guides per transcript & their titration candidates'.format(NUM_TOP_GUIDES)
+    # titration='Top {:d} guides per transcript & their titration candidates'.format(NUM_TOP_GUIDES)  # TODO: do this!
 )