Fix support for VCF sequence indexes

nextstrain · Jun 17, 2023 · 27afe62 · 27afe62
1 parent e885c95
commit 27afe62
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Showing 2 changed files with 17 additions and 5 deletions.
diff --git a/augur/filter/io.py b/augur/filter/io.py
@@ -146,7 +146,12 @@ def import_sequence_index(args):
 
     # Load the sequence index, if a path exists.
     if sequence_index_path:
-        sequence_index = TabularFile(sequence_index_path, header=True, delimiters=[SEQUENCE_INDEX_DELIMITER])
+        try:
+            sequence_index = TabularFile(sequence_index_path, header=True, delimiters=[SEQUENCE_INDEX_DELIMITER])
+        except InvalidDelimiter:
+            # This can happen for single-column files (e.g. VCF sequence indexes).
+            # If so, use a tab character as an arbitrary delimiter.
+            sequence_index = TabularFile(sequence_index_path, header=True, delimiter='\t')
         with Sqlite3Database(constants.RUNTIME_DB_FILE, mode="rw") as db:
             # Import the sequence index.
             _import_tabular_file(sequence_index, db, constants.SEQUENCE_INDEX_TABLE)

diff --git a/augur/io/tabular_file.py b/augur/io/tabular_file.py
@@ -24,13 +24,15 @@ class TabularFile(File):
     context-specific usage.
     """
 
-    def __init__(self, path: str, delimiters: Iterable[str] = None,
+    def __init__(self, path: str, delimiter: str = None, delimiters: Iterable[str] = None,
                  header: bool = False, columns: Iterable[str] = None):
         """
         Parameters
         ----------
         path
             Path of tabular file.
+        delimiter
+            Use this as the delimiter.
         delimiters
             List of possible delimiters to use, in order of precedence.
         header
@@ -40,11 +42,16 @@ def __init__(self, path: str, delimiters: Iterable[str] = None,
         """
         super().__init__(path)
 
-        if delimiters is None:
+        if delimiter and delimiters:
+            raise ValueError("At most one of delimiter and delimiters can be set.")
+
+        if not delimiter and not delimiters:
             delimiters = DEFAULT_DELIMITERS
 
-        self.delimiter = get_delimiter(self.path, delimiters)
-        """Delimiter of tabular file."""
+        if delimiter:
+            self.delimiter = delimiter
+        else:
+            self.delimiter = get_delimiter(self.path, delimiters)
 
         if (not header and not columns) or (header and columns):
             raise ValueError("Tabular file must have either a header row or column names specified, but not both.")