msa-parsers 6.5.0 → 8.0.0

package/README.md

@@ -30,12 +30,15 @@ pnpm add msa-parsers
 
 ### Parsing MSA files
 
-The `parseMSA` function auto-detects the format:
+`parseMSA` sniffs the format from the content, not from the file name. FASTA and
+A3M share a leading `>`, so telling them apart is heuristic; pass a format as
+the third argument to override the guess:
 
 ```typescript
 import { parseMSA } from 'msa-parsers'
 
 const msa = parseMSA(fileContents)
+const stockholm = parseMSA(fileContents, 0, 'stockholm')
 
 // Get sequence names
 const names = msa.getNames()
@@ -56,7 +59,8 @@ const tree = msa.getTree()
 import { FastaMSA, StockholmMSA, ClustalMSA } from 'msa-parsers'
 
 const fasta = new FastaMSA(fastaContents)
-const stockholm = new StockholmMSA(stockholmContents)
+// a Stockholm file can hold several alignments; the second argument picks one
+const stockholm = new StockholmMSA(stockholmContents, 0)
 const clustal = new ClustalMSA(clustalContents)
 ```
 
@@ -71,15 +75,26 @@ const treeWithIds = generateNodeIds(tree)
 
 ### GFF and InterProScan utilities
 
+Every source of overlay annotations converts to one flat list of `Annotation` (a
+row name, an accession, a name, a description and a 1-based inclusive interval),
+and the viewer draws that list.
+
 ```typescript
-import { parseGFF, gffToInterProResults, interProToGFF } from 'msa-parsers'
+import {
+  annotationsToGFF,
+  gffToAnnotations,
+  interProScanResponseToAnnotations,
+  parseGFF,
+} from 'msa-parsers'
+
+// GFF3 (including InterProScan's own output) to annotations
+const annotations = gffToAnnotations(parseGFF(gffContents))
 
-// Parse GFF file
-const records = parseGFF(gffContents)
+// an InterProScan JSON response to the same shape
+const fromScan = interProScanResponseToAnnotations(response)
 
-// Convert between GFF and InterProScan formats
-const interProResults = gffToInterProResults(records)
-const gffString = interProToGFF(interProResults, seqId)
+// and back out as GFF3, with optional `#` header lines
+const gffString = annotationsToGFF(annotations, ['written by my pipeline'])
 ```
 
 ## License

package/dist/gff/annotationsToGFF.d.ts

@@ -1,9 +1,11 @@
 import type { Annotation } from '../types.ts';
 /**
- * Write annotations as GFF3, one line per annotation, in list order.
+ * Write annotations as GFF3, one line per annotation, in list order, with
+ * optional `#` comment lines after the version directive saying where they came
+ * from.
  *
  * The source column is always `InterProScan`: an Annotation records no source
- * of its own, and the CLI's precomputed-lookup path depends on this output
- * matching what a real InterProScan run emits, byte for byte.
+ * of its own, and the viewer reads a precomputed-lookup GFF by the same rules
+ * it reads a real InterProScan run's.
  */
-export declare function annotationsToGFF(annotations: Annotation[]): string;
+export declare function annotationsToGFF(annotations: Annotation[], header?: string[]): string;

package/dist/gff/annotationsToGFF.js

@@ -1,13 +1,16 @@
 /**
- * Write annotations as GFF3, one line per annotation, in list order.
+ * Write annotations as GFF3, one line per annotation, in list order, with
+ * optional `#` comment lines after the version directive saying where they came
+ * from.
  *
  * The source column is always `InterProScan`: an Annotation records no source
- * of its own, and the CLI's precomputed-lookup path depends on this output
- * matching what a real InterProScan run emits, byte for byte.
+ * of its own, and the viewer reads a precomputed-lookup GFF by the same rules
+ * it reads a real InterProScan run's.
  */
-export function annotationsToGFF(annotations) {
+export function annotationsToGFF(annotations, header = []) {
     return [
         '##gff-version 3',
+        ...header.map(line => `# ${line}`),
         ...annotations.map(annotation => {
             const { accession, name, description, featureType } = annotation;
             const { id, start, end, strand } = annotation;

package/dist/gff/annotationsToGFF.js.map

@@ -1 +1 @@
-{"version":3,"file":"annotationsToGFF.js","sourceRoot":"","sources":["../../src/gff/annotationsToGFF.ts"],"names":[],"mappings":"AAEA;;;;;;GAMG;AACH,MAAM,UAAU,gBAAgB,CAAC,WAAyB;IACxD,OAAO;QACL,iBAAiB;QACjB,GAAG,WAAW,CAAC,GAAG,CAAC,UAAU,CAAC,EAAE;YAC9B,MAAM,EAAE,SAAS,EAAE,IAAI,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,UAAU,CAAA;YAChE,MAAM,EAAE,EAAE,EAAE,KAAK,EAAE,GAAG,EAAE,MAAM,EAAE,GAAG,UAAU,CAAA;YAC7C,OAAO;gBACL,EAAE;gBACF,cAAc;gBACd,mEAAmE;gBACnE,oEAAoE;gBACpE,gEAAgE;gBAChE,oCAAoC;gBACpC,WAAW,IAAI,eAAe;gBAC9B,KAAK;gBACL,GAAG;gBACH,GAAG;gBACH,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG;gBACnD,GAAG;gBACH;oBACE,QAAQ,kBAAkB,CAAC,SAAS,CAAC,EAAE;oBACvC,kBAAkB,kBAAkB,CAAC,IAAI,CAAC,EAAE;oBAC5C,eAAe,kBAAkB,CAAC,WAAW,CAAC,EAAE;iBACjD,CAAC,IAAI,CAAC,GAAG,CAAC;aACZ,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACd,CAAC,CAAC;KACH,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;AACd,CAAC"}
+{"version":3,"file":"annotationsToGFF.js","sourceRoot":"","sources":["../../src/gff/annotationsToGFF.ts"],"names":[],"mappings":"AAEA;;;;;;;;GAQG;AACH,MAAM,UAAU,gBAAgB,CAC9B,WAAyB,EACzB,MAAM,GAAa,EAAE;IAErB,OAAO;QACL,iBAAiB;QACjB,GAAG,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,KAAK,IAAI,EAAE,CAAC;QAClC,GAAG,WAAW,CAAC,GAAG,CAAC,UAAU,CAAC,EAAE;YAC9B,MAAM,EAAE,SAAS,EAAE,IAAI,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,UAAU,CAAA;YAChE,MAAM,EAAE,EAAE,EAAE,KAAK,EAAE,GAAG,EAAE,MAAM,EAAE,GAAG,UAAU,CAAA;YAC7C,OAAO;gBACL,EAAE;gBACF,cAAc;gBACd,mEAAmE;gBACnE,oEAAoE;gBACpE,gEAAgE;gBAChE,oCAAoC;gBACpC,WAAW,IAAI,eAAe;gBAC9B,KAAK;gBACL,GAAG;gBACH,GAAG;gBACH,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG;gBACnD,GAAG;gBACH;oBACE,QAAQ,kBAAkB,CAAC,SAAS,CAAC,EAAE;oBACvC,kBAAkB,kBAAkB,CAAC,IAAI,CAAC,EAAE;oBAC5C,eAAe,kBAAkB,CAAC,WAAW,CAAC,EAAE;iBACjD,CAAC,IAAI,CAAC,GAAG,CAAC;aACZ,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACd,CAAC,CAAC;KACH,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;AACd,CAAC"}

package/dist/gff/gffToAnnotations.js

@@ -22,6 +22,41 @@ function geneStrand({ type, strand }) {
     const directional = strand === '+' ? 1 : strand === '-' ? -1 : undefined;
     return GENE_LEVEL_TYPES.has(type) ? directional : undefined;
 }
+// The nine columns a feature line holds; every other key of a record came from
+// column 9
+const GFF_COLUMNS = new Set([
+    'seq_id',
+    'source',
+    'type',
+    'start',
+    'end',
+    'score',
+    'strand',
+    'phase',
+]);
+function attributesOf(record) {
+    const entries = Object.entries(record).filter(([key, value]) => !GFF_COLUMNS.has(key) && typeof value === 'string');
+    return entries.length > 0 ? Object.fromEntries(entries) : undefined;
+}
+// JBrowse and IGV read an RGB triple as well as a named or hex color, and the
+// attribute parser has already turned `255,0,0` into `255 0 0` by splitting on
+// the GFF3 multi-value comma
+const RGB_TRIPLE = /^(\d{1,3})[\s,]+(\d{1,3})[\s,]+(\d{1,3})$/;
+function cssColor(record) {
+    const value = (record.color ??
+        record.colour ??
+        record.Color ??
+        record.Colour);
+    if (!value) {
+        return undefined;
+    }
+    const triple = RGB_TRIPLE.exec(value.trim());
+    return triple ? `rgb(${triple[1]},${triple[2]},${triple[3]})` : value.trim();
+}
+// InterProScan describes the sequence it scanned before listing the matches
+// against it. Those lines span the whole row and carry no signature, so they
+// would draw a full-width block labelled by an md5.
+const WHOLE_SEQUENCE_TYPES = new Set(['polypeptide', 'nucleic_acid']);
 /**
  * Convert GFF records to annotations, one per record, in file order.
  *
@@ -30,23 +65,32 @@ function geneStrand({ type, strand }) {
  * name, with domain positions 1-based.
  */
 export function gffToAnnotations(gffRecords) {
-    return gffRecords.map(record => {
+    return gffRecords
+        .filter(record => !WHOLE_SEQUENCE_TYPES.has(record.type))
+        .map(record => {
         const accession = record.Name ||
             record.ID ||
             `${record.source}_${record.start}_${record.end}`;
-        const name = record.signature_desc || record.Name || accession;
+        const name = record.signature_desc ||
+            record.Name ||
+            accession;
         return {
             id: record.seq_id,
             accession,
             name,
-            description: record.Ontology_term ||
-                record.description ||
+            // not Ontology_term: a GO id list is what the domain is annotated
+            // with, not what it is, and reading it first labelled every
+            // InterProScan domain "GO:0003677 GO:0006281"
+            description: record.description ||
                 record.Note ||
+                record.signature_desc ||
                 name,
             featureType: record.type,
             start: record.start,
             end: record.end,
             strand: geneStrand(record),
+            color: cssColor(record),
+            attributes: attributesOf(record),
         };
     });
 }

package/dist/gff/gffToAnnotations.js.map

@@ -1 +1 @@
-{"version":3,"file":"gffToAnnotations.js","sourceRoot":"","sources":["../../src/gff/gffToAnnotations.ts"],"names":[],"mappings":"AAEA,8EAA8E;AAC9E,+EAA+E;AAC/E,gFAAgF;AAChF,uDAAuD;AACvD,MAAM,gBAAgB,GAAG,IAAI,GAAG,CAAC;IAC/B,MAAM;IACN,YAAY;IACZ,MAAM;IACN,YAAY;IACZ,oBAAoB;IACpB,OAAO;IACP,MAAM;IACN,MAAM;IACN,OAAO;IACP,QAAQ;IACR,OAAO;IACP,SAAS;CACV,CAAC,CAAA;AAEF,0EAA0E;AAC1E,oCAAoC;AACpC,SAAS,UAAU,CAAC,EAAE,IAAI,EAAE,MAAM,EAAa;IAC7C,MAAM,WAAW,GAAG,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACxE,OAAO,gBAAgB,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAAA;AAC7D,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,gBAAgB,CAAC,UAAuB;IACtD,OAAO,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;QAC7B,MAAM,SAAS,GACZ,MAAM,CAAC,IAAe;YACtB,MAAM,CAAC,EAAa;YACrB,GAAG,MAAM,CAAC,MAAM,IAAI,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,GAAG,EAAE,CAAA;QAClD,MAAM,IAAI,GACP,MAAM,CAAC,cAAyB,IAAK,MAAM,CAAC,IAAe,IAAI,SAAS,CAAA;QAC3E,OAAO;YACL,EAAE,EAAE,MAAM,CAAC,MAAM;YACjB,SAAS;YACT,IAAI;YACJ,WAAW,EACR,MAAM,CAAC,aAAwB;gBAC/B,MAAM,CAAC,WAAsB;gBAC7B,MAAM,CAAC,IAAe;gBACvB,IAAI;YACN,WAAW,EAAE,MAAM,CAAC,IAAI;YACxB,KAAK,EAAE,MAAM,CAAC,KAAK;YACnB,GAAG,EAAE,MAAM,CAAC,GAAG;YACf,MAAM,EAAE,UAAU,CAAC,MAAM,CAAC;SAC3B,CAAA;IACH,CAAC,CAAC,CAAA;AACJ,CAAC"}
+{"version":3,"file":"gffToAnnotations.js","sourceRoot":"","sources":["../../src/gff/gffToAnnotations.ts"],"names":[],"mappings":"AAEA,8EAA8E;AAC9E,+EAA+E;AAC/E,gFAAgF;AAChF,uDAAuD;AACvD,MAAM,gBAAgB,GAAG,IAAI,GAAG,CAAC;IAC/B,MAAM;IACN,YAAY;IACZ,MAAM;IACN,YAAY;IACZ,oBAAoB;IACpB,OAAO;IACP,MAAM;IACN,MAAM;IACN,OAAO;IACP,QAAQ;IACR,OAAO;IACP,SAAS;CACV,CAAC,CAAA;AAEF,0EAA0E;AAC1E,oCAAoC;AACpC,SAAS,UAAU,CAAC,EAAE,IAAI,EAAE,MAAM,EAAa;IAC7C,MAAM,WAAW,GAAG,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACxE,OAAO,gBAAgB,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAAA;AAC7D,CAAC;AAED,+EAA+E;AAC/E,WAAW;AACX,MAAM,WAAW,GAAG,IAAI,GAAG,CAAC;IAC1B,QAAQ;IACR,QAAQ;IACR,MAAM;IACN,OAAO;IACP,KAAK;IACL,OAAO;IACP,QAAQ;IACR,OAAO;CACR,CAAC,CAAA;AAEF,SAAS,YAAY,CAAC,MAAiB;IACrC,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,MAAM,CAC3C,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,OAAO,KAAK,KAAK,QAAQ,CAC/C,CAAA;IACvB,OAAO,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;AACrE,CAAC;AAED,8EAA8E;AAC9E,+EAA+E;AAC/E,6BAA6B;AAC7B,MAAM,UAAU,GAAG,2CAA2C,CAAA;AAE9D,SAAS,QAAQ,CAAC,MAAiB;IACjC,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,KAAK;QACzB,MAAM,CAAC,MAAM;QACb,MAAM,CAAC,KAAK;QACZ,MAAM,CAAC,MAAM,CAAuB,CAAA;IACtC,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,MAAM,GAAG,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAA;IAC5C,OAAO,MAAM,CAAC,CAAC,CAAC,OAAO,MAAM,CAAC,CAAC,CAAC,IAAI,MAAM,CAAC,CAAC,CAAC,IAAI,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,EAAE,CAAA;AAC9E,CAAC;AAED,4EAA4E;AAC5E,6EAA6E;AAC7E,oDAAoD;AACpD,MAAM,oBAAoB,GAAG,IAAI,GAAG,CAAC,CAAC,aAAa,EAAE,cAAc,CAAC,CAAC,CAAA;AAErE;;;;;;GAMG;AACH,MAAM,UAAU,gBAAgB,CAAC,UAAuB;IACtD,OAAO,UAAU;SACd,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC,oBAAoB,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;SACxD,GAAG,CAAC,MAAM,CAAC,EAAE;QACZ,MAAM,SAAS,GACZ,MAAM,CAAC,IAAe;YACtB,MAAM,CAAC,EAAa;YACrB,GAAG,MAAM,CAAC,MAAM,IAAI,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,GAAG,EAAE,CAAA;QAClD,MAAM,IAAI,GACP,MAAM,CAAC,cAAyB;YAChC,MAAM,CAAC,IAAe;YACvB,SAAS,CAAA;QACX,OAAO;YACL,EAAE,EAAE,MAAM,CAAC,MAAM;YACjB,SAAS;YACT,IAAI;YACJ,kEAAkE;YAClE,4DAA4D;YAC5D,8CAA8C;YAC9C,WAAW,EACR,MAAM,CAAC,WAAsB;gBAC7B,MAAM,CAAC,IAAe;gBACtB,MAAM,CAAC,cAAyB;gBACjC,IAAI;YACN,WAAW,EAAE,MAAM,CAAC,IAAI;YACxB,KAAK,EAAE,MAAM,CAAC,KAAK;YACnB,GAAG,EAAE,MAAM,CAAC,GAAG;YACf,MAAM,EAAE,UAAU,CAAC,MAAM,CAAC;YAC1B,KAAK,EAAE,QAAQ,CAAC,MAAM,CAAC;YACvB,UAAU,EAAE,YAAY,CAAC,MAAM,CAAC;SACjC,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}

package/dist/gff/parseGFF.js

@@ -8,6 +8,11 @@ function safeDecode(val) {
         return val;
     }
 }
+// InterProScan quotes some of its values (Ontology_term="GO:0008652",
+// Dbxref="InterPro:IPR001048"), and the quotes are not part of the term
+function unquote(val) {
+    return val.replace(/^"(.*)"$/, '$1');
+}
 function parseAttributes(col9) {
     if (!col9) {
         return {};
@@ -28,7 +33,7 @@ function parseAttributes(col9) {
             val
                 ? val
                     .split(',')
-                    .map(v => safeDecode(v).trim())
+                    .map(v => unquote(safeDecode(v).trim()))
                     .join(' ')
                 : undefined,
         ];
@@ -39,11 +44,21 @@ export function parseGFF(str) {
     if (!str) {
         return [];
     }
-    return str
-        .split('\n')
-        .map(f => f.trim())
-        .filter(f => !!f && !f.startsWith('#'))
-        .map(f => {
+    const lines = [];
+    for (const raw of str.split('\n')) {
+        const line = raw.trim();
+        // InterProScan appends the sequences it scanned; every line past this is
+        // FASTA, and reading it as features gave rows named ">P51587"
+        if (line.startsWith('##FASTA')) {
+            break;
+        }
+        // a feature is nine tab-separated columns, eight of them mandatory; a
+        // FASTA line in a file that omitted the ##FASTA directive is one
+        if (line && !line.startsWith('#') && line.split('\t').length >= 8) {
+            lines.push(line);
+        }
+    }
+    return lines.map(f => {
         const parts = f.split('\t');
         const [seq_id, source, type, start, end, score, strand, phase] = parts;
         const col9 = parts[8];

package/dist/gff/parseGFF.js.map

@@ -1 +1 @@
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package/dist/interProScanToAnnotations.d.ts

@@ -10,8 +10,13 @@ export declare function indexResultsByXref(results: InterProScanResults[]): {
 };
 /**
  * Flatten InterProScan results, keyed by the row name they attach to, into one
- * annotation per signature location. A signature without an `entry` carries no
- * accession or name to color, filter or label by, so it is dropped.
+ * annotation per signature location.
+ *
+ * An unintegrated signature has no InterPro `entry` -- MobiDBLite's disorder
+ * calls, and many CDD, Pfam and PANTHER hits -- and falling back to the
+ * signature's own accession and name is the difference between drawing those
+ * and dropping them. Only a signature with no accession at all has nothing to
+ * color, filter or label by, and is dropped.
  */
 export declare function interProScanToAnnotations(results: Record<string, InterProScanResults>): Annotation[];
 /**

package/dist/interProScanToAnnotations.js

@@ -11,22 +11,32 @@ export function indexResultsByXref(results) {
 }
 /**
  * Flatten InterProScan results, keyed by the row name they attach to, into one
- * annotation per signature location. A signature without an `entry` carries no
- * accession or name to color, filter or label by, so it is dropped.
+ * annotation per signature location.
+ *
+ * An unintegrated signature has no InterPro `entry` -- MobiDBLite's disorder
+ * calls, and many CDD, Pfam and PANTHER hits -- and falling back to the
+ * signature's own accession and name is the difference between drawing those
+ * and dropping them. Only a signature with no accession at all has nothing to
+ * color, filter or label by, and is dropped.
  */
 export function interProScanToAnnotations(results) {
-    return Object.entries(results).flatMap(([id, { matches }]) => matches.flatMap(({ signature: { entry }, locations }) => entry
-        ? locations.map(({ start, end, strand }) => ({
+    return Object.entries(results).flatMap(([id, { matches }]) => matches.flatMap(({ signature, locations }) => {
+        const { entry } = signature;
+        const accession = entry?.accession ?? signature.accession;
+        if (!accession) {
+            return [];
+        }
+        const name = entry?.name ?? signature.name ?? accession;
+        return locations.map(({ start, end, strand }) => ({
             id,
-            accession: entry.accession,
-            name: entry.name,
-            description: entry.description,
-            featureType: entry.featureType,
+            accession,
+            name,
+            description: entry?.description ?? signature.description ?? name,
             start,
             end,
             strand,
-        }))
-        : []));
+        }));
+    }));
 }
 /**
  * Flatten a whole InterProScan JSON response, resolving each result's row name

package/dist/interProScanToAnnotations.js.map

@@ -1 +1 @@
-{"version":3,"file":"interProScanToAnnotations.js","sourceRoot":"","sources":["../src/interProScanToAnnotations.ts"],"names":[],"mappings":"AAMA;;;;;GAKG;AACH,MAAM,UAAU,kBAAkB,CAAC,OAA8B;IAC/D,OAAO,MAAM,CAAC,WAAW,CACvB,OAAO;SACJ,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAU,CAAC;SACrC,MAAM,CAAC,CAAC,CAAC,EAAsC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACzE,CAAA;AACH,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,yBAAyB,CACvC,OAA4C;IAE5C,OAAO,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,OAAO,EAAE,CAAC,EAAE,EAAE,CAC3D,OAAO,CAAC,OAAO,CAAC,CAAC,EAAE,SAAS,EAAE,EAAE,KAAK,EAAE,EAAE,SAAS,EAAE,EAAE,EAAE,CACtD,KAAK;QACH,CAAC,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,GAAG,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAAC;YACzC,EAAE;YACF,SAAS,EAAE,KAAK,CAAC,SAAS;YAC1B,IAAI,EAAE,KAAK,CAAC,IAAI;YAChB,WAAW,EAAE,KAAK,CAAC,WAAW;YAC9B,WAAW,EAAE,KAAK,CAAC,WAAW;YAC9B,KAAK;YACL,GAAG;YACH,MAAM;SACP,CAAC,CAAC;QACL,CAAC,CAAC,EAAE,CACP,CACF,CAAA;AACH,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,iCAAiC,CAC/C,QAA8B;IAE9B,OAAO,yBAAyB,CAAC,kBAAkB,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAA;AACxE,CAAC"}
+{"version":3,"file":"interProScanToAnnotations.js","sourceRoot":"","sources":["../src/interProScanToAnnotations.ts"],"names":[],"mappings":"AAMA;;;;;GAKG;AACH,MAAM,UAAU,kBAAkB,CAAC,OAA8B;IAC/D,OAAO,MAAM,CAAC,WAAW,CACvB,OAAO;SACJ,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAU,CAAC;SACrC,MAAM,CAAC,CAAC,CAAC,EAAsC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACzE,CAAA;AACH,CAAC;AAED;;;;;;;;;GASG;AACH,MAAM,UAAU,yBAAyB,CACvC,OAA4C;IAE5C,OAAO,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,OAAO,EAAE,CAAC,EAAE,EAAE,CAC3D,OAAO,CAAC,OAAO,CAAC,CAAC,EAAE,SAAS,EAAE,SAAS,EAAE,EAAE,EAAE;QAC3C,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAA;QAC3B,MAAM,SAAS,GAAG,KAAK,EAAE,SAAS,IAAI,SAAS,CAAC,SAAS,CAAA;QACzD,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,IAAI,GAAG,KAAK,EAAE,IAAI,IAAI,SAAS,CAAC,IAAI,IAAI,SAAS,CAAA;QACvD,OAAO,SAAS,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,GAAG,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAAC;YAChD,EAAE;YACF,SAAS;YACT,IAAI;YACJ,WAAW,EAAE,KAAK,EAAE,WAAW,IAAI,SAAS,CAAC,WAAW,IAAI,IAAI;YAChE,KAAK;YACL,GAAG;YACH,MAAM;SACP,CAAC,CAAC,CAAA;IACL,CAAC,CAAC,CACH,CAAA;AACH,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,iCAAiC,CAC/C,QAA8B;IAE9B,OAAO,yBAAyB,CAAC,kBAAkB,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAA;AACxE,CAAC"}

package/dist/msa/A3mMSA.js

@@ -1,5 +1,5 @@
 import BaseMSA from './BaseMSA.js';
-import { splitFastaRecords } from './fastaRecords.js';
+import { fastaSniff, splitFastaRecords } from './fastaRecords.js';
 /**
  * A3M Format Parser
  *
@@ -61,7 +61,7 @@ export default class A3mMSA extends BaseMSA {
         };
     }
     static sniff(text) {
-        if (!text.startsWith('>')) {
+        if (!fastaSniff(text)) {
             return false;
         }
         const seqs = splitFastaRecords(text)
@@ -114,7 +114,7 @@ function expandA3M(rawSeqs, names) {
             maxInserts[pos] = Math.max(maxInserts[pos], ins.length);
         }
     }
-    const expanded = {};
+    const expanded = Object.create(null);
     for (const [seqIdx, { matches, inserts }] of rows.entries()) {
         const result = [];
         for (let pos = 0; pos <= numPositions; pos++) {

package/dist/msa/A3mMSA.js.map

@@ -1 +1 @@
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package/dist/msa/BaseMSA.d.ts

@@ -1,17 +1,13 @@
-import type { NodeWithIds } from '../types.ts';
+import type { MSATrack, NodeWithIds } from '../types.ts';
 export default abstract class BaseMSA {
     abstract getMSA(): unknown;
     abstract getRow(name: string): string;
     abstract getNames(): string[];
     private width?;
     /**
-     * Column count of the alignment: the length of its widest row.
-     *
-     * Not the first row's length. Ragged input is real -- a hand-edited fasta, or
-     * an aligner that stops a row at its last residue -- and taking row 0 makes
-     * every column past it unreachable when row 0 is the short one. The viewer's
-     * gap analysis already defines the column count this way, so anything else
-     * disagrees with it.
+     * Column count of the alignment: the length of its widest row, since a
+     * hand-edited fasta or some aligners leave rows short. The viewer's gap
+     * analysis counts columns the same way.
      */
     getWidth(): number;
     getTree(): NodeWithIds;
@@ -25,10 +21,5 @@ export default abstract class BaseMSA {
     get alignmentNames(): string[];
     get seqConsensus(): string | undefined;
     get secondaryStructureConsensus(): string | undefined;
-    get tracks(): {
-        id: string;
-        name: string;
-        data?: string;
-        customColorScheme?: Record<string, string>;
-    }[];
+    get tracks(): MSATrack[];
 }

package/dist/msa/BaseMSA.js

@@ -1,13 +1,9 @@
 export default class BaseMSA {
     width;
     /**
-     * Column count of the alignment: the length of its widest row.
-     *
-     * Not the first row's length. Ragged input is real -- a hand-edited fasta, or
-     * an aligner that stops a row at its last residue -- and taking row 0 makes
-     * every column past it unreachable when row 0 is the short one. The viewer's
-     * gap analysis already defines the column count this way, so anything else
-     * disagrees with it.
+     * Column count of the alignment: the length of its widest row, since a
+     * hand-edited fasta or some aligners leave rows short. The viewer's gap
+     * analysis counts columns the same way.
      */
     getWidth() {
         this.width ??= this.getNames().reduce((max, name) => Math.max(max, this.getRow(name).length), 0);

package/dist/msa/BaseMSA.js.map

@@ -1 +1 @@
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+{"version":3,"file":"BaseMSA.js","sourceRoot":"","sources":["../../src/msa/BaseMSA.ts"],"names":[],"mappings":"AAEA,MAAM,CAAC,OAAO,OAAgB,OAAO;IAK3B,KAAK,CAAS;IAEtB;;;;OAIG;IACH,QAAQ;QACN,IAAI,CAAC,KAAK,KAAK,IAAI,CAAC,QAAQ,EAAE,CAAC,MAAM,CACnC,CAAC,GAAG,EAAE,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,EACtD,CAAC,CACF,CAAA;QACD,OAAO,IAAI,CAAC,KAAK,CAAA;IACnB,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACrC,EAAE,EAAE,IAAI;gBACR,QAAQ,EAAE,EAAE;gBACZ,IAAI;aACL,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,UAAU,CACR,KAAa;QAEb,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,SAAS;QACP,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,YAAY;QACd,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}

package/dist/msa/FastaMSA.js

@@ -8,8 +8,8 @@ export default class FastaMSA extends BaseMSA {
     constructor(text) {
         super();
         const records = splitFastaRecords(text);
-        const seqdata = {};
-        const colonNormalized = {};
+        const seqdata = Object.create(null);
+        const colonNormalized = Object.create(null);
         for (const { id, seq } of records) {
             seqdata[id] = seq;
             if (id.includes(':')) {

package/dist/msa/FastaMSA.js.map

@@ -1 +1 @@
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package/dist/msa/StockholmMSA.d.ts

@@ -1,5 +1,5 @@
 import BaseMSA from './BaseMSA.ts';
-import type { NodeWithIds } from '../types.ts';
+import type { MSATrack, NodeWithIds } from '../types.ts';
 import type { StockholmData } from './stockholmParser.ts';
 export default class StockholmMSA extends BaseMSA {
     private data;
@@ -32,11 +32,11 @@ export default class StockholmMSA extends BaseMSA {
     getTree(): NodeWithIds;
     get seqConsensus(): string | undefined;
     get secondaryStructureConsensus(): string | undefined;
-    get tracks(): {
-        id: string;
-        name: string;
-        data?: string;
-        customColorScheme?: Record<string, string>;
-    }[];
+    /**
+     * One text track per `#=GC` line, and one per `#=GR` line that stays hidden
+     * until asked for: a Pfam seed carries a few per-row active-site lines, but
+     * an Rfam family carries a structure line for every row with a PDB entry.
+     */
+    get tracks(): MSATrack[];
 }
 export { sniff as stockholmSniff } from './stockholmParser.ts';

package/dist/msa/StockholmMSA.js

@@ -46,7 +46,7 @@ export default class StockholmMSA extends BaseMSA {
         return this.MSA.seqname;
     }
     getStructures() {
-        const pdbRegex = /PDB; +(\S+) +(\S); ([0-9]+)-([0-9]+)/;
+        const pdbRegex = /PDB; +(\S+) +([^;\s]+); *(-?[0-9]+)-(-?[0-9]+)/;
         const drEntries = this.MSA.gs.DR ?? {};
         const result = {};
         for (const [id, drList] of Object.entries(drEntries)) {
@@ -75,35 +75,58 @@ export default class StockholmMSA extends BaseMSA {
     get secondaryStructureConsensus() {
         return this.MSA.gc.SS_cons;
     }
+    /**
+     * One text track per `#=GC` line, and one per `#=GR` line that stays hidden
+     * until asked for: a Pfam seed carries a few per-row active-site lines, but
+     * an Rfam family carries a structure line for every row with a PDB entry.
+     */
     get tracks() {
+        const { seq_cons, SS_cons, ...otherGc } = this.MSA.gc;
         return [
             {
                 id: 'seqConsensus',
                 name: 'Sequence consensus',
-                data: this.seqConsensus,
+                data: seq_cons,
                 customColorScheme: {},
             },
             {
                 id: 'secondaryStruct',
                 name: 'Secondary-structure',
-                data: this.secondaryStructureConsensus,
-                // WUSS notation pairs base-paired columns as open/close brackets of
-                // several nesting types (<>, (), [], {}); color all opens one way and
-                // closes the other so every helix (e.g. the tRNA acceptor stem, which
-                // is written with parens) is highlighted, not just the <> arms.
-                customColorScheme: {
-                    '<': 'lightblue',
-                    '(': 'lightblue',
-                    '[': 'lightblue',
-                    '{': 'lightblue',
-                    '>': 'pink',
-                    ')': 'pink',
-                    ']': 'pink',
-                    '}': 'pink',
-                },
+                data: SS_cons,
+                customColorScheme: wussColors,
             },
+            ...Object.entries(otherGc).map(([tag, data]) => ({
+                id: `gc-${tag}`,
+                name: tag,
+                data,
+                customColorScheme: structureColors(tag),
+            })),
+            ...Object.entries(this.MSA.gr).flatMap(([tag, byRow]) => Object.entries(byRow).map(([row, data]) => ({
+                id: `gr-${row}-${tag}`,
+                name: `${row} ${tag}`,
+                data,
+                customColorScheme: structureColors(tag),
+                defaultOff: true,
+            }))),
         ];
     }
 }
+// WUSS writes base-paired columns as open/close brackets of several nesting
+// types (<>, (), [], {}); coloring every open one way and every close the other
+// highlights each helix, including the tRNA acceptor stem written with parens
+const wussColors = {
+    '<': 'lightblue',
+    '(': 'lightblue',
+    '[': 'lightblue',
+    '{': 'lightblue',
+    '>': 'pink',
+    ')': 'pink',
+    ']': 'pink',
+    '}': 'pink',
+};
+// `SS`, and Rfam's per-structure `2GIS_A_SS`
+function structureColors(tag) {
+    return tag === 'SS' || tag.endsWith('_SS') ? wussColors : {};
+}
 export { sniff as stockholmSniff } from './stockholmParser.js';
 //# sourceMappingURL=StockholmMSA.js.map

package/dist/msa/StockholmMSA.js.map

@@ -1 +1 @@
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package/dist/msa/fastaRecords.d.ts

@@ -2,10 +2,15 @@ export interface FastaRecord {
     id: string;
     seq: string;
 }
+export declare function fastaSniff(text: string): boolean;
 /**
  * Split FASTA-style text (shared by the FASTA and A3M parsers) into records.
- * The id is the defline up to the first space. A repeated id keeps the first
- * record: ids index the row data, so emitting the id twice would render a
- * phantom duplicate row showing the last record's residues.
+ *
+ * A record starts at a `>` that begins a line, so a `>` inside a defline
+ * (`x->y`, HGVS `c.1799T>A`) stays part of it, and anything before the first
+ * record (ColabFold's `#8\t1` header) is skipped. The id is the defline up to
+ * the first whitespace, tab included. A repeated id keeps the first record: ids
+ * index the row data, so emitting the id twice would render a phantom duplicate
+ * row showing the last record's residues.
  */
 export declare function splitFastaRecords(text: string): FastaRecord[];