add params json

sanjaynagi · Oct 11, 2024 · ba3b5d2 · ba3b5d2
1 parent afc6033
commit ba3b5d2
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Showing 3 changed files with 72 additions and 0 deletions.
diff --git a/AnoPrimer/params/default.json b/AnoPrimer/params/default.json
@@ -0,0 +1,23 @@
+{
+    "PRIMER_TASK": "generic",
+
+    "PRIMER_MIN_SIZE": 17,
+    "PRIMER_OPT_SIZE": 20,
+    "PRIMER_MAX_SIZE": 24,
+
+    "PRIMER_MIN_GC": 30,
+    "PRIMER_MAX_GC": 70,
+    "PRIMER_INTERNAL_MIN_GC": 10,
+
+    "PRIMER_MIN_TM": 57.0,
+    "PRIMER_OPT_TM": 60.0,
+    "PRIMER_MAX_TM": 63.0,
+
+    "PRIMER_MIN_THREE_PRIME_DISTANCE": 3,
+
+    "PRIMER_INTERNAL_OPT_SIZE": 16,
+    "PRIMER_INTERNAL_MIN_SIZE": 10,
+    "PRIMER_INTERNAL_MAX_SIZE": 22,
+    "PRIMER_INTERNAL_MIN_TM": 45,
+    "PRIMER_INTERNAL_MAX_TM": 65
+}
diff --git a/AnoPrimer/params/relaxed.json b/AnoPrimer/params/relaxed.json
@@ -0,0 +1,23 @@
+{
+    "PRIMER_TASK": "generic",
+
+    "PRIMER_MIN_SIZE": 18,
+    "PRIMER_OPT_SIZE": 20,
+    "PRIMER_MAX_SIZE": 27,
+
+    "PRIMER_MIN_GC": 20,
+    "PRIMER_MAX_GC": 80,
+    "PRIMER_INTERNAL_MIN_GC": 10,
+
+    "PRIMER_MIN_TM": 55.0,
+    "PRIMER_OPT_TM": 60.0,
+    "PRIMER_MAX_TM": 64.0,
+
+    "PRIMER_MIN_THREE_PRIME_DISTANCE": 2,
+
+    "PRIMER_INTERNAL_OPT_SIZE": 16,
+    "PRIMER_INTERNAL_MIN_SIZE": 10,
+    "PRIMER_INTERNAL_MAX_SIZE": 22,
+    "PRIMER_INTERNAL_MIN_TM": 45,
+    "PRIMER_INTERNAL_MAX_TM": 65
+}
diff --git a/AnoPrimer/params/stringent.json b/AnoPrimer/params/stringent.json
@@ -0,0 +1,26 @@
+{
+    "PRIMER_TASK": "generic",
+
+    "PRIMER_MIN_SIZE": 18,
+    "PRIMER_OPT_SIZE": 20,
+    "PRIMER_MAX_SIZE": 27,
+
+    "PRIMER_MIN_GC": 20,
+    "PRIMER_MAX_GC": 80,
+    "PRIMER_INTERNAL_MIN_GC": 10,
+
+    "PRIMER_MIN_TM": 57.0,
+    "PRIMER_OPT_TM": 60.0,
+    "PRIMER_MAX_TM": 63.0,
+    "PRIMER_PAIR_MAX_DIFF_TM": 2.0,
+
+    "PRIMER_MAX_SELF_ANY": 8.0,
+    "PRIMER_MAX_SELF_END": 1.0,
+
+    "PRIMER_PAIR_MAX_COMPL_ANY": 8.0,
+    "PRIMER_PAIR_MAX_COMPL_END": 1.0,
+
+    "PRIMER_INTERNAL_MAX_POLY_X": 5,
+
+    "PRIMER_MIN_THREE_PRIME_DISTANCE": 3
+}