@teselagen/sequence-utils 0.3.32 → 0.3.36

package/calculateEndStability.d.ts

@@ -0,0 +1,16 @@
+/**
+ * Calculate End Stability (3' end stability) of a primer
+ *
+ * The maximum stability for the last five 3' bases of a left or right primer.
+ * Bigger numbers mean more stable 3' ends. The value is the maximum delta G
+ * (kcal/mol) for duplex disruption for the five 3' bases.
+ *
+ * According to Primer3 documentation:
+ * - Most stable 5mer duplex: GCGCG = 6.86 kcal/mol (SantaLucia 1998)
+ * - Most labile 5mer duplex: TATAT = 0.86 kcal/mol (SantaLucia 1998)
+ *
+ * @param {string} sequence - DNA sequence (5' to 3')
+ * @returns {number} - Delta G (kcal/mol) for the last 5 bases at 3' end
+ * @throws {Error} Invalid sequence or too short.
+ */
+export default function calculateEndStability(sequence: string): number;

package/calculateEndStability.test.d.ts

@@ -0,0 +1 @@
+export {};

package/calculateSantaLuciaTm.d.ts

@@ -0,0 +1,127 @@
+/**
+ * Validate DNA sequence
+ *
+ * @param {string} sequence - DNA sequence
+ * @returns {boolean} - True if valid
+ */
+export function isValidSequence(sequence: string): boolean;
+/**
+ * Calculate melting temperature using SantaLucia (1998) method
+ *
+ * @param {string} sequence - DNA sequence (5' to 3')
+ * @returns {number} - Melting temperature in Celsius
+ * @throws {Error} Invalid sequence or too short.
+ */
+export default function calculateSantaLuciaTm(sequence: string): number;
+export namespace SANTA_LUCIA_NN {
+    namespace AA {
+        let dH: number;
+        let dS: number;
+    }
+    namespace TT {
+        let dH_1: number;
+        export { dH_1 as dH };
+        let dS_1: number;
+        export { dS_1 as dS };
+    }
+    namespace AT {
+        let dH_2: number;
+        export { dH_2 as dH };
+        let dS_2: number;
+        export { dS_2 as dS };
+    }
+    namespace TA {
+        let dH_3: number;
+        export { dH_3 as dH };
+        let dS_3: number;
+        export { dS_3 as dS };
+    }
+    namespace CA {
+        let dH_4: number;
+        export { dH_4 as dH };
+        let dS_4: number;
+        export { dS_4 as dS };
+    }
+    namespace TG {
+        let dH_5: number;
+        export { dH_5 as dH };
+        let dS_5: number;
+        export { dS_5 as dS };
+    }
+    namespace GT {
+        let dH_6: number;
+        export { dH_6 as dH };
+        let dS_6: number;
+        export { dS_6 as dS };
+    }
+    namespace AC {
+        let dH_7: number;
+        export { dH_7 as dH };
+        let dS_7: number;
+        export { dS_7 as dS };
+    }
+    namespace CT {
+        let dH_8: number;
+        export { dH_8 as dH };
+        let dS_8: number;
+        export { dS_8 as dS };
+    }
+    namespace AG {
+        let dH_9: number;
+        export { dH_9 as dH };
+        let dS_9: number;
+        export { dS_9 as dS };
+    }
+    namespace GA {
+        let dH_10: number;
+        export { dH_10 as dH };
+        let dS_10: number;
+        export { dS_10 as dS };
+    }
+    namespace TC {
+        let dH_11: number;
+        export { dH_11 as dH };
+        let dS_11: number;
+        export { dS_11 as dS };
+    }
+    namespace CG {
+        let dH_12: number;
+        export { dH_12 as dH };
+        let dS_12: number;
+        export { dS_12 as dS };
+    }
+    namespace GC {
+        let dH_13: number;
+        export { dH_13 as dH };
+        let dS_13: number;
+        export { dS_13 as dS };
+    }
+    namespace GG {
+        let dH_14: number;
+        export { dH_14 as dH };
+        let dS_14: number;
+        export { dS_14 as dS };
+    }
+    namespace CC {
+        let dH_15: number;
+        export { dH_15 as dH };
+        let dS_15: number;
+        export { dS_15 as dS };
+    }
+}
+export namespace SANTA_LUCIA_INIT {
+    export namespace GC_1 {
+        let dH_16: number;
+        export { dH_16 as dH };
+        let dS_16: number;
+        export { dS_16 as dS };
+    }
+    export { GC_1 as GC };
+    export namespace AT_1 {
+        let dH_17: number;
+        export { dH_17 as dH };
+        let dS_17: number;
+        export { dS_17 as dS };
+    }
+    export { AT_1 as AT };
+}

package/calculateSantaLuciaTm.test.d.ts

@@ -0,0 +1 @@
+export {};

package/diffUtils.d.ts

@@ -1,7 +1,7 @@
 export function getDiffFromSeqs(oldData: any, newData: any, { ignoreKeys }?: {
     ignoreKeys?: never[] | undefined;
-}): any;
+}): import('jsondiffpatch').Delta;
 export function patchSeqWithDiff(oldData: any, diff: any, { ignoreKeys }?: {
     ignoreKeys?: never[] | undefined;
-}): any;
-export function reverseSeqDiff(diff: any): any;
+}): unknown;
+export function reverseSeqDiff(diff: any): import('jsondiffpatch').Delta;