update the spec to enable zero length regions and zero length sequenc…

…es when min_len is zero
pachterlab · Aug 7, 2024 · 7c1a6a5 · 7c1a6a5
1 parent 19298dc
commit 7c1a6a5
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Showing 2 changed files with 28 additions and 5 deletions.
diff --git a/seqspec/Region.py b/seqspec/Region.py
@@ -75,9 +75,9 @@ def update_attr(self):
         self.sequence = self.get_sequence()
         self.min_len, self.max_len = self.get_len()
         if self.sequence_type == "random":
-            self.sequence = "X" * self.max_len
+            self.sequence = "X" * self.min_len
         if self.sequence_type == "onlist":
-            self.sequence = "N" * self.max_len
+            self.sequence = "N" * self.min_len
         return
 
     def __repr__(self) -> str:

diff --git a/seqspec/schema/seqspec.schema.json b/seqspec/schema/seqspec.schema.json
@@ -144,8 +144,7 @@
         },
         "sequence": {
           "description": "The sequence",
-          "type": "string",
-          "pattern": "^[ACGTRYMKSWHBVDNX]+$"
+          "type": "string"
         },
         "min_len": {
           "description": "The minimum length of the sequence",
@@ -194,7 +193,31 @@
         "sequence",
         "min_len",
         "max_len"
-      ]
+      ],
+      "if": {
+        "properties": {
+          "min_len": {
+            "const": 0
+          }
+        }
+      },
+      "then": {
+        "properties": {
+          "sequence": {
+            "type": "string",
+            "pattern": "^[ACGTRYMKSWHBVDNX]*$"
+          }
+        }
+      },
+      "else": {
+        "properties": {
+          "sequence": {
+            "type": "string",
+            "minLength": 1,
+            "pattern": "^[ACGTRYMKSWHBVDNX]+$"
+          }
+        }
+      }
     },
     "read": {
       "title": "Read",