jbrowse-plugin-protein3d 0.0.2

package/dist/mappings.d.ts

@@ -0,0 +1,19 @@
+import { Feature } from '@jbrowse/core/util';
+export interface Alignment {
+    alns: {
+        id: string;
+        seq: string;
+    }[];
+}
+export declare function structureSeqVsTranscriptSeqMap(alignment: Alignment): {
+    structureSeqToTranscriptSeqPosition: Record<string, number | undefined>;
+    transcriptSeqToStructureSeqPosition: Record<string, number | undefined>;
+};
+export declare function structurePositionToAlignmentMap(alignment: Alignment): Record<string, number | undefined>;
+export declare function transcriptPositionToAlignmentMap(alignment: Alignment): Record<string, number | undefined>;
+export declare function genomeToTranscriptSeqMapping(feature: Feature): {
+    g2p: Record<number, number | undefined>;
+    p2g: Record<number, number | undefined>;
+    refName: string;
+    strand: number;
+};

package/dist/mappings.js

@@ -0,0 +1,67 @@
+import { genomeToTranscriptSeqMapping as g2p } from 'g2p_mapper';
+export function structureSeqVsTranscriptSeqMap(alignment) {
+    const structureSeq = alignment.alns[0].seq;
+    const transcriptSeq = alignment.alns[1].seq;
+    if (structureSeq.length !== transcriptSeq.length) {
+        throw new Error('mismatched length');
+    }
+    let j = 0;
+    let k = 0;
+    const structureSeqToTranscriptSeqPosition = {};
+    const transcriptSeqToStructureSeqPosition = {};
+    // eslint-disable-next-line unicorn/no-for-loop
+    for (let i = 0; i < structureSeq.length; i++) {
+        const c1 = structureSeq[i];
+        const c2 = transcriptSeq[i];
+        if (c1 === c2) {
+            structureSeqToTranscriptSeqPosition[j] = k;
+            transcriptSeqToStructureSeqPosition[k] = j;
+            k++;
+            j++;
+        }
+        else if (c2 === '-') {
+            j++;
+        }
+        else if (c1 === '-') {
+            k++;
+        }
+        else {
+            structureSeqToTranscriptSeqPosition[j] = k;
+            transcriptSeqToStructureSeqPosition[k] = j;
+            k++;
+            j++;
+        }
+    }
+    return {
+        structureSeqToTranscriptSeqPosition,
+        transcriptSeqToStructureSeqPosition,
+    };
+}
+export function structurePositionToAlignmentMap(alignment) {
+    const structureSeq = alignment.alns[0].seq;
+    const structurePositionToAlignment = {};
+    for (let i = 0, j = 0; i < structureSeq.length; i++) {
+        if (structureSeq[i] !== '-') {
+            structurePositionToAlignment[j] = i;
+            j++;
+        }
+    }
+    return structurePositionToAlignment;
+}
+export function transcriptPositionToAlignmentMap(alignment) {
+    const transcriptSeq = alignment.alns[1].seq;
+    const transcriptPositionToAlignment = {};
+    for (let i = 0, j = 0; i < transcriptSeq.length; i++) {
+        if (transcriptSeq[i] !== '-') {
+            transcriptPositionToAlignment[j] = i;
+            j++;
+        }
+    }
+    return transcriptPositionToAlignment;
+}
+// see similar function in msaview plugin
+export function genomeToTranscriptSeqMapping(feature) {
+    // @ts-expect-error
+    return g2p(feature.toJSON());
+}
+//# sourceMappingURL=mappings.js.map

package/dist/mappings.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"mappings.js","sourceRoot":"","sources":["../src/mappings.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,4BAA4B,IAAI,GAAG,EAAE,MAAM,YAAY,CAAA;AAShE,MAAM,UAAU,8BAA8B,CAAC,SAAoB;IACjE,MAAM,YAAY,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAC1C,MAAM,aAAa,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAC3C,IAAI,YAAY,CAAC,MAAM,KAAK,aAAa,CAAC,MAAM,EAAE,CAAC;QACjD,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;IACtC,CAAC;IAED,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,MAAM,mCAAmC,GAAG,EAG3C,CAAA;IACD,MAAM,mCAAmC,GAAG,EAG3C,CAAA;IAED,+CAA+C;IAC/C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC7C,MAAM,EAAE,GAAG,YAAY,CAAC,CAAC,CAAC,CAAA;QAC1B,MAAM,EAAE,GAAG,aAAa,CAAC,CAAC,CAAC,CAAA;QAE3B,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC;YACd,mCAAmC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,mCAAmC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,CAAC,EAAE,CAAA;YACH,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE,CAAC;YACtB,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE,CAAC;YACtB,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,CAAC;YACN,mCAAmC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,mCAAmC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YAE1C,CAAC,EAAE,CAAA;YACH,CAAC,EAAE,CAAA;QACL,CAAC;IACH,CAAC;IACD,OAAO;QACL,mCAAmC;QACnC,mCAAmC;KACpC,CAAA;AACH,CAAC;AAED,MAAM,UAAU,+BAA+B,CAAC,SAAoB;IAClE,MAAM,YAAY,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAC1C,MAAM,4BAA4B,GAAG,EAAwC,CAAA;IAE7E,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACpD,IAAI,YAAY,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YAC5B,4BAA4B,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YACnC,CAAC,EAAE,CAAA;QACL,CAAC;IACH,CAAC;IAED,OAAO,4BAA4B,CAAA;AACrC,CAAC;AAED,MAAM,UAAU,gCAAgC,CAAC,SAAoB;IACnE,MAAM,aAAa,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAC3C,MAAM,6BAA6B,GAAG,EAAwC,CAAA;IAE9E,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACrD,IAAI,aAAa,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YAC7B,6BAA6B,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YACpC,CAAC,EAAE,CAAA;QACL,CAAC;IACH,CAAC;IAED,OAAO,6BAA6B,CAAA;AACtC,CAAC;AAED,yCAAyC;AACzC,MAAM,UAAU,4BAA4B,CAAC,OAAgB;IAC3D,mBAAmB;IACnB,OAAO,GAAG,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC,CAAA;AAC9B,CAAC"}

package/dist/mappings.test.d.ts

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

package/dist/mappings.test.js

@@ -0,0 +1,27 @@
+import { genomeToTranscriptSeqMapping, structureSeqVsTranscriptSeqMap, } from './mappings';
+import { SimpleFeature } from '@jbrowse/core/util';
+import { feature, alignment } from './test_data/gene';
+test('test', () => {
+    const ret = structureSeqVsTranscriptSeqMap(alignment);
+    expect(ret).toMatchSnapshot();
+});
+test('mapping', () => {
+    const res = genomeToTranscriptSeqMapping(new SimpleFeature(feature));
+    const { p2g } = res;
+    const aln = structureSeqVsTranscriptSeqMap(alignment);
+    // expected position in sequence
+    const s2 = alignment.alns[1].seq;
+    expect(s2[392]).toBe('M');
+    expect(s2[393]).toBe('K');
+    expect(s2[394]).toBe('A');
+    expect(s2[395]).toBe('A');
+    // maps the 392 position in the "pdb version of the protein" to the 0th
+    // position in the genome version of the protein, and then maps that back to
+    // the genome
+    const p0 = aln.structureSeqToTranscriptSeqPosition[392];
+    const g0 = p2g[p0];
+    expect(p0).toBe(0);
+    expect(g0).toBe(51_296_155);
+    expect(res).toMatchSnapshot();
+});
+//# sourceMappingURL=mappings.test.js.map

package/dist/mappings.test.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"mappings.test.js","sourceRoot":"","sources":["../src/mappings.test.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,4BAA4B,EAC5B,8BAA8B,GAC/B,MAAM,YAAY,CAAA;AACnB,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA;AAClD,OAAO,EAAE,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAA;AAErD,IAAI,CAAC,MAAM,EAAE,GAAG,EAAE;IAChB,MAAM,GAAG,GAAG,8BAA8B,CAAC,SAAS,CAAC,CAAA;IACrD,MAAM,CAAC,GAAG,CAAC,CAAC,eAAe,EAAE,CAAA;AAC/B,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,SAAS,EAAE,GAAG,EAAE;IACnB,MAAM,GAAG,GAAG,4BAA4B,CAAC,IAAI,aAAa,CAAC,OAAO,CAAC,CAAC,CAAA;IACpE,MAAM,EAAE,GAAG,EAAE,GAAG,GAAG,CAAA;IACnB,MAAM,GAAG,GAAG,8BAA8B,CAAC,SAAS,CAAC,CAAA;IAErD,gCAAgC;IAChC,MAAM,EAAE,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAChC,MAAM,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACzB,MAAM,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACzB,MAAM,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACzB,MAAM,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACzB,uEAAuE;IACvE,4EAA4E;IAC5E,aAAa;IACb,MAAM,EAAE,GAAG,GAAG,CAAC,mCAAmC,CAAC,GAAG,CAAE,CAAA;IACxD,MAAM,EAAE,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IAClB,MAAM,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAClB,MAAM,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;IAC3B,MAAM,CAAC,GAAG,CAAC,CAAC,eAAe,EAAE,CAAA;AAC/B,CAAC,CAAC,CAAA"}

package/dist/test_data/gene.d.ts

@@ -0,0 +1,67 @@
+export declare const feature: {
+    strand: number;
+    source: string;
+    type: string;
+    start: number;
+    end: number;
+    phase: number;
+    derived_features: never[];
+    refName: string;
+    id: string;
+    parent: string;
+    gene_id: string;
+    transcript_id: string;
+    gene_type: string;
+    gene_name: string;
+    transcript_type: string;
+    transcript_name: string;
+    level: string;
+    protein_id: string;
+    transcript_support_level: string;
+    hgnc_id: string;
+    tag: string[];
+    ccdsid: string;
+    havana_gene: string;
+    havana_transcript: string;
+    subfeatures: {
+        strand: number;
+        source: string;
+        type: string;
+        start: number;
+        end: number;
+        phase: number;
+        derived_features: never[];
+        refName: string;
+        id: string;
+        parent: string;
+        gene_id: string;
+        transcript_id: string;
+        gene_type: string;
+        gene_name: string;
+        transcript_type: string;
+        transcript_name: string;
+        exon_number: string;
+        exon_id: string;
+        level: string;
+        protein_id: string;
+        transcript_support_level: string;
+        hgnc_id: string;
+        tag: string[];
+        ccdsid: string;
+        havana_gene: string;
+        havana_transcript: string;
+        uniqueId: string;
+        parentId: string;
+        __jbrowsefmt: {};
+    }[];
+    uniqueId: string;
+    parentId: string;
+    __jbrowsefmt: {};
+};
+export declare const alignment: {
+    consensus: string;
+    alns: {
+        id: string;
+        seq: string;
+    }[];
+};