Fix paths --fasta SQL query.

The SQL query was completely wrong. It was most likely meant to work
with an earlier version of the schema.

1 files changed, 4 insertions, 3 deletions

diff --git a/domagi/domagi.py b/domagi/domagi.py
index c9d3ee2..6981132 100644
--- a/domagi/domagi.py
+++ b/domagi/domagi.py
@@ -276,10 +276,11 @@ def paths(con, list_paths, fasta, threads):
             print(name)
     elif fasta:
         for name, sequence in con.execute("""
-        SELECT ANY_VALUE(path_name),
-               string_agg(sequence, '' ORDER BY position)
-        FROM path
+        SELECT ANY_VALUE(path.name),
+               string_agg(sequence, '' ORDER BY start)
+        FROM path_segment
         INNER JOIN segment ON segment.id = path_segment.segment_id
+        INNER JOIN path ON path.id = path_segment.path_id
         GROUP BY path_id
         """).fetchall():
             print(f">{name}")