add --check-unknown-nucleotides flag

bin/proviral.py

@@ -53,6 +53,9 @@ def cli():
 @click.option(
     '--check-internal-inversion/--ignore-internal-inversion', default=False
 )
+@click.option(
+    '--check-unknown-nucleotides/--ignore-unknown-nucleotides', default=True
+)
 @click.option(
     '--include-small-orfs/--exclude-small-orfs', default=False)
 @click.option(
@@ -65,7 +68,7 @@ def cli():
 def intact(input_file, subtype, include_packaging_signal,
            include_rre, check_major_splice_donor_site, run_hypermut,
            check_long_deletion, check_nonhiv, check_scramble, check_internal_inversion,
-           include_small_orfs, output_csv, working_folder):
+           check_unknown_nucleotides, include_small_orfs, output_csv, working_folder):
     """
     Check consensus sequences for intactness.
     """
@@ -77,7 +80,7 @@ def intact(input_file, subtype, include_packaging_signal,
         folder, input_file, subtype, include_packaging_signal, include_rre,
         check_major_splice_donor_site, run_hypermut,
         check_long_deletion, check_nonhiv, check_scramble, check_internal_inversion,
-        include_small_orfs, output_csv
+        check_unknown_nucleotides, include_small_orfs, output_csv
     )
 
 if __name__ == "__main__": cli()

intact/intact.py

@@ -711,6 +711,7 @@ def intact( working_dir,
             check_nonhiv,
             check_scramble,
             check_internal_inversion,
+            check_unknown_nucleotides,
             include_small_orfs,
             output_csv,
             hxb2_forward_orfs = const.DEFAULT_FORWARD_ORFs,

tests/test_end_to_end.py

@@ -19,6 +19,7 @@ def run_end_to_end(tmp_path, data_file, expected_dir, subtype, output_csv):
         check_nonhiv=True,
         check_scramble=True,
         check_internal_inversion=True,
+        check_unknown_nucleotides=True,
         include_small_orfs=True,
         output_csv=output_csv,
         )