msa-parsers 8.2.0 → 8.3.0

package/dist/msa/StockholmMSA.js.map

@@ -1 +1 @@
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+{"version":3,"file":"StockholmMSA.js","sourceRoot":"","sources":["../../src/msa/StockholmMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,MAAM,YAAY,CAAA;AAC5C,OAAO,OAAO,MAAM,cAAc,CAAA;AAClC,OAAO,WAAW,MAAM,kBAAkB,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAA;AAK/C,MAAM,CAAC,OAAO,OAAO,YAAa,SAAQ,OAAO;IACvC,IAAI,CAAiB;IACrB,GAAG,CAAe;IAE1B,YAAY,IAAY,EAAE,gBAAwB;QAChD,MAAM,GAAG,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC1B,MAAM,GAAG,GAAG,GAAG,CAAC,gBAAgB,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,CAAA;QAC3C,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,MAAM,IAAI,KAAK,CAAC,uCAAuC,CAAC,CAAA;QAC1D,CAAC;QACD,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,EAAE,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAA;QAC/D,IAAI,CAAC,IAAI,GAAG,GAAG,CAAA;QACf,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;IAChB,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,aAAa,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IAC9E,CAAC;IAED,SAAS;QACP,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,OAAO;YACL,OAAO,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE;YACpB,UAAU,EAAE,MAAM,CAAC,WAAW,CAC5B,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CACrD;YACD,MAAM,EAAE,MAAM,CAAC,WAAW,CACxB,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAC7D;SACF,CAAA;IACH,CAAC;IAED,UAAU,CAAC,OAAe;QACxB,OAAO;YACL,IAAI,EAAE,OAAO;YACb,SAAS,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC;YACzC,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC;SAC9C,CAAA;IACH,CAAC;IAED,aAAa;QACX,MAAM,QAAQ,GAAG,gDAAgD,CAAA;QACjE,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,MAAM,MAAM,GAGR,EAAE,CAAA;QACN,KAAK,MAAM,CAAC,EAAE,EAAE,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE,CAAC;YACrD,KAAK,MAAM,EAAE,IAAI,MAAM,EAAE,CAAC;gBACxB,MAAM,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAC/B,IAAI,KAAK,EAAE,CAAC;oBACV,CAAC;oBAAA,CAAC,MAAM,CAAC,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC,IAAI,CAAC;wBACxB,GAAG,EAAE,KAAK,CAAC,CAAC,CAAE,CAAC,WAAW,EAAE;wBAC5B,KAAK,EAAE,KAAK,CAAC,CAAC,CAAE;wBAChB,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;wBACpB,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;qBACnB,CAAC,CAAA;gBACJ,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC;IAED,OAAO;QACL,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAA;QAChC,OAAO,IAAI,CAAC,CAAC,CAAC,eAAe,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,EAAE,CAAA;IACpE,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,QAAQ,CAAA;IAC7B,CAAC;IAED,IAAI,2BAA2B;QAC7B,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,OAAO,CAAA;IAC5B,CAAC;IAED;;;;OAIG;IACH,IAAI,MAAM;QACR,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,GAAG,OAAO,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAA;QACrD,OAAO;YACL;gBACE,EAAE,EAAE,cAAc;gBAClB,IAAI,EAAE,oBAAoB;gBAC1B,IAAI,EAAE,QAAQ;gBACd,iBAAiB,EAAE,EAAE;aACtB;YACD;gBACE,EAAE,EAAE,iBAAiB;gBACrB,IAAI,EAAE,qBAAqB;gBAC3B,IAAI,EAAE,OAAO;gBACb,iBAAiB,EAAE,UAAU;aAC9B;YACD,GAAG,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,CAAC,CAAC;gBAC/C,EAAE,EAAE,MAAM,GAAG,EAAE;gBACf,IAAI,EAAE,GAAG;gBACT,IAAI;gBACJ,iBAAiB,EAAE,eAAe,CAAC,GAAG,CAAC;aACxC,CAAC,CAAC;YACH,GAAG,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CACtD,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,CAAC,CAAC;gBAC1C,EAAE,EAAE,MAAM,GAAG,IAAI,GAAG,EAAE;gBACtB,IAAI,EAAE,GAAG,GAAG,IAAI,GAAG,EAAE;gBACrB,IAAI;gBACJ,iBAAiB,EAAE,eAAe,CAAC,GAAG,CAAC;gBACvC,UAAU,EAAE,IAAI;aACjB,CAAC,CAAC,CACJ;SACF,CAAA;IACH,CAAC;CACF;AAED,4EAA4E;AAC5E,gFAAgF;AAChF,8EAA8E;AAC9E,MAAM,UAAU,GAA2B;IACzC,GAAG,EAAE,WAAW;IAChB,GAAG,EAAE,WAAW;IAChB,GAAG,EAAE,WAAW;IAChB,GAAG,EAAE,WAAW;IAChB,GAAG,EAAE,MAAM;IACX,GAAG,EAAE,MAAM;IACX,GAAG,EAAE,MAAM;IACX,GAAG,EAAE,MAAM;CACZ,CAAA;AAED,6CAA6C;AAC7C,SAAS,eAAe,CAAC,GAAW;IAClC,OAAO,GAAG,KAAK,IAAI,IAAI,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAA;AAC9D,CAAC;AAED,OAAO,EAAE,KAAK,IAAI,cAAc,EAAE,MAAM,sBAAsB,CAAA"}

package/dist/msa/fastaRecords.d.ts

@@ -8,9 +8,11 @@ export declare function fastaSniff(text: string): boolean;
  *
  * 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.
+ * record (ColabFold's `#8\t1` header) is skipped. The id is the first word of
+ * the defline, so `> name` reads as `name`, and a defline with no word names
+ * its record `unnamed_N` after its position in the file. 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[];
+export declare function toRecords(input: string | FastaRecord[]): FastaRecord[];

package/dist/msa/fastaRecords.js

@@ -7,10 +7,11 @@ export function fastaSniff(text) {
  *
  * 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.
+ * record (ColabFold's `#8\t1` header) is skipped. The id is the first word of
+ * the defline, so `> name` reads as `name`, and a defline with no word names
+ * its record `unnamed_N` after its position in the file. 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 function splitFastaRecords(text) {
     const records = [];
@@ -25,11 +26,13 @@ export function splitFastaRecords(text) {
             });
         }
     };
+    let count = 0;
     for (const line of text.split('\n')) {
         if (line.startsWith('>')) {
             flush();
-            const id = /^>(\S*)/.exec(line)[1];
-            current = id ? { id, lines: [] } : undefined;
+            count++;
+            const id = /^>\s*(\S*)/.exec(line)[1] || `unnamed_${count}`;
+            current = { id, lines: [] };
         }
         else {
             current?.lines.push(line);
@@ -38,4 +41,7 @@ export function splitFastaRecords(text) {
     flush();
     return records;
 }
+export function toRecords(input) {
+    return typeof input === 'string' ? splitFastaRecords(input) : input;
+}
 //# sourceMappingURL=fastaRecords.js.map

package/dist/msa/fastaRecords.js.map

@@ -1 +1 @@
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+{"version":3,"file":"fastaRecords.js","sourceRoot":"","sources":["../../src/msa/fastaRecords.ts"],"names":[],"mappings":"AAKA,8EAA8E;AAC9E,MAAM,UAAU,UAAU,CAAC,IAAY;IACrC,OAAO,YAAY,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;AAChC,CAAC;AAED;;;;;;;;;;GAUG;AACH,MAAM,UAAU,iBAAiB,CAAC,IAAY;IAC5C,MAAM,OAAO,GAAkB,EAAE,CAAA;IACjC,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAA;IAC9B,IAAI,OAAoD,CAAA;IAExD,MAAM,KAAK,GAAG,GAAG,EAAE;QACjB,IAAI,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,EAAE,CAAC;YACrC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;YACpB,OAAO,CAAC,IAAI,CAAC;gBACX,EAAE,EAAE,OAAO,CAAC,EAAE;gBACd,GAAG,EAAE,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC;aAClD,CAAC,CAAA;QACJ,CAAC;IACH,CAAC,CAAA;IAED,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,KAAK,MAAM,IAAI,IAAI,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC;QACpC,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YACzB,KAAK,EAAE,CAAA;YACP,KAAK,EAAE,CAAA;YACP,MAAM,EAAE,GAAG,YAAY,CAAC,IAAI,CAAC,IAAI,CAAE,CAAC,CAAC,CAAC,IAAI,WAAW,KAAK,EAAE,CAAA;YAC5D,OAAO,GAAG,EAAE,EAAE,EAAE,KAAK,EAAE,EAAE,EAAE,CAAA;QAC7B,CAAC;aAAM,CAAC;YACN,OAAO,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAC3B,CAAC;IACH,CAAC;IACD,KAAK,EAAE,CAAA;IAEP,OAAO,OAAO,CAAA;AAChB,CAAC;AAED,MAAM,UAAU,SAAS,CAAC,KAA6B;IACrD,OAAO,OAAO,KAAK,KAAK,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAA;AACrE,CAAC"}

package/dist/msa/index.js

@@ -3,16 +3,18 @@ import ClustalMSA from './ClustalMSA.js';
 import EmfMSA from './EmfMSA.js';
 import FastaMSA from './FastaMSA.js';
 import StockholmMSA, { stockholmSniff } from './StockholmMSA.js';
-import { fastaSniff } from './fastaRecords.js';
+import { fastaSniff, splitFastaRecords } from './fastaRecords.js';
 export { parseEmfTree } from 'emf-js';
 export { default as parseNewick } from './parseNewick.js';
 const htmlPage = /^<(!doctype\s+html|html[\s>])/i;
-// when `format` is given the heuristic sniffing is bypassed -- callers that
-// already know the format (e.g. impg emitting fasta-aln) can force it rather
-// than rely on auto-detection, which is necessarily ambiguous between formats
-// that share a leading '>' (fasta vs a3m)
+const clustalHeader = /^(CLUSTAL|MUSCLE|PROBCONS|MSAPROBS|Kalign)/i;
+// A caller that knows the format, such as impg emitting fasta-aln, passes
+// `format` to skip sniffing, which cannot always tell FASTA from A3M
 export function parseMSA(input, currentAlignment = 0, format) {
-    const text = input.replace(/^\uFEFF/, '').trimStart();
+    const text = input
+        .replace(/^\uFEFF/, '')
+        .replaceAll(/\r\n?/g, '\n')
+        .trimStart();
     if (htmlPage.test(text)) {
         throw new Error('Received an HTML page, not an alignment. Check that the URL points at the file itself');
     }
@@ -34,16 +36,20 @@ export function parseMSA(input, currentAlignment = 0, format) {
     if (stockholmSniff(text)) {
         return new StockholmMSA(text, currentAlignment);
     }
-    if (A3mMSA.sniff(text)) {
-        return new A3mMSA(text);
-    }
     if (fastaSniff(text)) {
-        return new FastaMSA(text);
+        const records = splitFastaRecords(text);
+        return A3mMSA.sniff(records) ? new A3mMSA(records) : new FastaMSA(records);
     }
     if (text.startsWith('SEQ')) {
         return new EmfMSA(text);
     }
-    return new ClustalMSA(text);
+    if (clustalHeader.test(text)) {
+        return new ClustalMSA(text);
+    }
+    const firstLine = text.split('\n', 1)[0].slice(0, 80);
+    throw new Error(firstLine
+        ? `Unrecognized alignment format: expected FASTA, A3M, Stockholm, Clustal or EMF, but the first line reads "${firstLine}"`
+        : 'The alignment file is empty');
 }
 /**
  * Get ungapped sequence from an aligned row

package/dist/msa/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/msa/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,aAAa,CAAA;AAChC,OAAO,UAAU,MAAM,iBAAiB,CAAA;AACxC,OAAO,MAAM,MAAM,aAAa,CAAA;AAChC,OAAO,QAAQ,MAAM,eAAe,CAAA;AACpC,OAAO,YAAY,EAAE,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAA;AAChE,OAAO,EAAE,UAAU,EAAE,iBAAiB,EAAE,MAAM,mBAAmB,CAAA;AAEjE,OAAO,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AACrC,OAAO,EAAE,OAAO,IAAI,WAAW,EAAE,MAAM,kBAAkB,CAAA;AAWzD,MAAM,QAAQ,GAAG,gCAAgC,CAAA;AACjD,MAAM,aAAa,GAAG,6CAA6C,CAAA;AAEnE,0EAA0E;AAC1E,qEAAqE;AACrE,MAAM,UAAU,QAAQ,CACtB,KAAa,EACb,gBAAgB,GAAG,CAAC,EACpB,MAAkB;IAElB,MAAM,IAAI,GAAG,KAAK;SACf,OAAO,CAAC,SAAS,EAAE,EAAE,CAAC;SACtB,UAAU,CAAC,QAAQ,EAAE,IAAI,CAAC;SAC1B,SAAS,EAAE,CAAA;IACd,IAAI,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;QACxB,MAAM,IAAI,KAAK,CACb,uFAAuF,CACxF,CAAA;IACH,CAAC;IACD,IAAI,MAAM,KAAK,WAAW,EAAE,CAAC;QAC3B,OAAO,IAAI,YAAY,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;IACjD,CAAC;IACD,IAAI,MAAM,KAAK,KAAK,EAAE,CAAC;QACrB,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,IAAI,MAAM,KAAK,OAAO,EAAE,CAAC;QACvB,OAAO,IAAI,QAAQ,CAAC,IAAI,CAAC,CAAA;IAC3B,CAAC;IACD,IAAI,MAAM,KAAK,KAAK,EAAE,CAAC;QACrB,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;QACzB,OAAO,IAAI,UAAU,CAAC,IAAI,CAAC,CAAA;IAC7B,CAAC;IACD,IAAI,cAAc,CAAC,IAAI,CAAC,EAAE,CAAC;QACzB,OAAO,IAAI,YAAY,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;IACjD,CAAC;IACD,IAAI,UAAU,CAAC,IAAI,CAAC,EAAE,CAAC;QACrB,MAAM,OAAO,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAA;QACvC,OAAO,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,QAAQ,CAAC,OAAO,CAAC,CAAA;IAC5E,CAAC;IACD,IAAI,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC;QAC3B,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,IAAI,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;QAC7B,OAAO,IAAI,UAAU,CAAC,IAAI,CAAC,CAAA;IAC7B,CAAC;IACD,MAAM,SAAS,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,CAAE,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAA;IACtD,MAAM,IAAI,KAAK,CACb,SAAS;QACP,CAAC,CAAC,4GAA4G,SAAS,GAAG;QAC1H,CAAC,CAAC,6BAA6B,CAClC,CAAA;AACH,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,mBAAmB,CAAC,UAAkB;IACpD,OAAO,UAAU,CAAC,UAAU,CAAC,OAAO,EAAE,EAAE,CAAC,CAAA;AAC3C,CAAC;AAED,OAAO,EAAE,OAAO,IAAI,MAAM,EAAE,MAAM,aAAa,CAAA;AAC/C,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,iBAAiB,CAAA;AACvD,OAAO,EAAE,OAAO,IAAI,MAAM,EAAE,MAAM,aAAa,CAAA;AAC/C,OAAO,EAAE,OAAO,IAAI,QAAQ,EAAE,MAAM,eAAe,CAAA;AACnD,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "msa-parsers",
-  "version": "8.2.0",
+  "version": "8.3.0",
   "license": "MIT",
   "type": "module",
   "repository": {

package/src/gff/annotationTextToGFF.ts

@@ -0,0 +1,17 @@
+import { interProScanResponseToAnnotations } from '../interProScanToAnnotations.ts'
+import { annotationsToGFF } from './annotationsToGFF.ts'
+
+import type { InterProScanResponse } from '../types.ts'
+
+/**
+ * An annotation file's text as GFF3: GFF passes through, and the JSON an
+ * InterProScan run returns converts, taking each result's row from its xref.
+ */
+export function annotationTextToGFF(text: string): string {
+  const trimmed = text.trimStart()
+  if (!trimmed.startsWith('{')) {
+    return text
+  }
+  const response: InterProScanResponse = JSON.parse(trimmed)
+  return annotationsToGFF(interProScanResponseToAnnotations(response))
+}

package/src/gff/annotationsToGFF.ts

@@ -20,7 +20,7 @@ export function annotationsToGFF(
       const { accession, name, description, featureType } = annotation
       const { id, start, end, strand } = annotation
       return [
-        id,
+        id.replaceAll(/[%\t\n\r]/g, encodeURIComponent),
         'InterProScan',
         // GFF-sourced annotations carry their original type; writing every
         // feature back out as protein_match would turn an exon overlay into

package/src/gff/gffToAnnotations.test.ts

@@ -68,6 +68,7 @@ test('gives gene-level features a direction but leaves exons/domains as blocks',
   const annotations = gffToAnnotations([
     record({ type: 'gene', strand: '+', Name: 'GENEA' }),
     record({ type: 'mRNA', strand: '-', Name: 'GENEB' }),
+    record({ type: 'CDS', strand: '-', Name: 'orfA' }),
     record({ type: 'exon', strand: '+', Name: 'exon-1' }),
     record({ type: 'protein_match', strand: '+', Name: 'PF00001' }),
   ])
@@ -76,6 +77,7 @@ test('gives gene-level features a direction but leaves exons/domains as blocks',
   ).toEqual({
     GENEA: 1, // + gene -> arrow right
     GENEB: -1, // - gene -> arrow left
+    orfA: -1, // a prokaryotic gene is a CDS row
     'exon-1': undefined, // exon stays a block even though it is stranded
     PF00001: undefined, // protein domain stays a block
   })

package/src/gff/gffToAnnotations.ts

@@ -1,11 +1,11 @@
 import type { Annotation, GFFRecord } from '../types.ts'
 
-// Feature types that read as a directional "gene" and get an arrowhead in the
-// overlay. Exon/CDS/UTR/domain features deliberately stay rectangular blocks —
-// turning every exon into an arrow is misleading, since exons are segments of a
-// single transcript, not independently-oriented genes.
+// Feature types drawn with an arrowhead for their strand. A prokaryotic GFF
+// writes each gene as a CDS row. Exon, UTR and domain features stay blocks,
+// since an exon is a segment of one transcript.
 const GENE_LEVEL_TYPES = new Set([
   'gene',
+  'CDS',
   'pseudogene',
   'mRNA',
   'transcript',

package/src/gff/interProToGFF.test.ts

@@ -189,6 +189,13 @@ describe('interProToGFF', () => {
     ])
   })
 
+  test('round-trips a row name holding a percent sign', () => {
+    const gff = annotationsToGFF(
+      gffToAnnotations(parseGFF('a%25b/1-9\tsrc\tgene\t1\t5\t.\t+\t.\tName=x')),
+    )
+    expect(parseGFF(gff)[0]?.seq_id).toBe('a%b/1-9')
+  })
+
   test('URL-encodes special characters in attributes', () => {
     const results: Record<string, InterProScanResults> = {
       seq1: {

package/src/gff/parseGFF.test.ts

@@ -111,6 +111,20 @@ MPIGSKERPTFFEIFKTRCNKADLGPISLN
     expect(result[0]?.Note).toBe('100%done')
   })
 
+  test('decodes a percent-encoded seq_id', () => {
+    const result = parseGFF(
+      'HBA%2FHUMAN/27-137\tsrc\tgene\t1\t5\t.\t+\t.\tName=x',
+    )
+    expect(result[0]?.seq_id).toBe('HBA/HUMAN/27-137')
+  })
+
+  test('drops an attribute with no value', () => {
+    const result = parseGFF('a\tsrc\tgene\t1\t5\t.\t+\t.\tName=x;flag;Note=')
+    expect(Object.keys(result[0]!)).not.toContain('flag')
+    expect(Object.keys(result[0]!)).not.toContain('Note')
+    expect(result[0]?.Name).toBe('x')
+  })
+
   test('keeps text after a second equals sign', () => {
     const gff = 'seq1\tSource\ttype\t1\t10\t.\t.\t.\tNote=a=b'
     const result = parseGFF(gff)

package/src/gff/parseGFF.ts

@@ -16,34 +16,26 @@ function unquote(val: string) {
   return val.replace(/^"(.*)"$/, '$1')
 }
 
-function parseAttributes(col9?: string): Record<string, string | undefined> {
+function parseAttributes(col9?: string): Record<string, string> {
   if (!col9) {
     return {}
   }
-  return Object.fromEntries(
-    col9
-      .split(';')
-      .map(f => f.trim())
-      .filter(f => !!f)
-      .map(f => {
-        const eq = f.indexOf('=')
-        const key = (eq === -1 ? f : f.slice(0, eq)).trim()
-        const val = eq === -1 ? undefined : f.slice(eq + 1)
-        // split on comma (the GFF3 multi-value separator) BEFORE decoding, so a
-        // literal comma encoded as %2C survives the split and isn't mistaken
-        // for a separator
-        return [
-          key,
-          val
-            ? val
-                .split(',')
-                .map(v => unquote(safeDecode(v).trim()))
-                .join(' ')
-            : undefined,
-        ]
-      })
-      .filter(([key]) => key !== ''),
-  )
+  const attributes: Record<string, string> = {}
+  for (const field of col9.split(';')) {
+    const eq = field.indexOf('=')
+    const key = field.slice(0, eq).trim()
+    const val = field.slice(eq + 1)
+    // split on comma (the GFF3 multi-value separator) BEFORE decoding, so a
+    // literal comma encoded as %2C survives the split and isn't mistaken
+    // for a separator
+    if (eq !== -1 && key && val) {
+      attributes[key] = val
+        .split(',')
+        .map(v => unquote(safeDecode(v).trim()))
+        .join(' ')
+    }
+  }
+  return attributes
 }
 
 export function parseGFF(str?: string): GFFRecord[] {
@@ -73,7 +65,7 @@ export function parseGFF(str?: string): GFFRecord[] {
     // "start=") can't turn a number field into a string
     return {
       ...parseAttributes(col9),
-      seq_id: seq_id ?? '',
+      seq_id: safeDecode(seq_id ?? ''),
       source: source ?? '',
       type: type ?? '',
       start: Number(start) || 0,

package/src/index.ts

@@ -34,3 +34,4 @@ export {
   interProToGFF,
   parseGFF,
 } from './gff/index.ts'
+export { annotationTextToGFF } from './gff/annotationTextToGFF.ts'

package/src/msa/A3mMSA.test.ts

@@ -1,6 +1,7 @@
 import { describe, expect, test } from 'vitest'
 
 import A3mMSA from './A3mMSA.ts'
+import { splitFastaRecords } from './fastaRecords.ts'
 
 // A3M format rules (see https://yanglab.qd.sdu.edu.cn/trRosetta/msa_format.html):
 //
@@ -68,6 +69,21 @@ ACDEF
 ACDEF---`
       expect(A3mMSA.sniff(notA3m)).toBe(false)
     })
+
+    test('returns false when rows with inserts differ in match columns', () => {
+      expect(A3mMSA.sniff('>a\nACDEFgh\n>b\nACDEFG\n')).toBe(false)
+    })
+
+    test('reads records split once by the caller', () => {
+      const a3m = '>seq1\nACDEFghiKLMNPQ\n>seq2\nACDEFKLMNPQ\n'
+      const records = splitFastaRecords(a3m)
+      expect(A3mMSA.sniff(records)).toBe(true)
+      const fromRecords = new A3mMSA(records)
+      const fromText = new A3mMSA(a3m)
+      expect(fromRecords.getNames()).toEqual(fromText.getNames())
+      expect(fromRecords.getRow('seq1')).toBe(fromText.getRow('seq1'))
+      expect(fromRecords.getRow('seq2')).toBe('ACDEF...KLMNPQ')
+    })
   })
 
   describe('parsing', () => {
@@ -294,18 +310,6 @@ ACDEF`
       expect(msa.getWidth()).toBe(5)
     })
 
-    test('getMSA returns seqdata', () => {
-      const a3m = `>seq1
-ACDEF
->seq2
-GHIKL`
-      const msa = new A3mMSA(a3m)
-      const data = msa.getMSA()
-
-      expect(data.seqdata).toHaveProperty('seq1')
-      expect(data.seqdata).toHaveProperty('seq2')
-    })
-
     test('getTree returns noTree structure', () => {
       const a3m = `>seq1
 ACDEF

package/src/msa/A3mMSA.ts

@@ -1,5 +1,7 @@
 import BaseMSA from './BaseMSA.ts'
-import { fastaSniff, splitFastaRecords } from './fastaRecords.ts'
+import { fastaSniff, toRecords } from './fastaRecords.ts'
+
+import type { FastaRecord } from './fastaRecords.ts'
 
 /**
  * A3M Format Parser
@@ -67,27 +69,18 @@ function parseRow(seq: string): ParsedRow {
 }
 
 export default class A3mMSA extends BaseMSA {
-  private MSA: { seqdata: Record<string, string> }
-  private orderedNames: string[]
-
-  constructor(text: string) {
-    super()
-    const records = splitFastaRecords(text)
-    this.orderedNames = records.map(r => r.id)
-    this.MSA = {
-      seqdata: expandA3M(
-        records.map(r => r.seq),
-        this.orderedNames,
-      ),
-    }
+  constructor(input: string | FastaRecord[]) {
+    const records = toRecords(input)
+    const expanded = expandA3M(records.map(r => r.seq))
+    super(records.map((r, i) => [r.id, expanded[i]!]))
   }
 
-  static sniff(text: string): boolean {
-    if (!fastaSniff(text)) {
+  static sniff(input: string | FastaRecord[]): boolean {
+    if (typeof input === 'string' && !fastaSniff(input)) {
       return false
     }
 
-    const seqs = splitFastaRecords(text)
+    const seqs = toRecords(input)
       .map(r => r.seq)
       .filter(s => !!s)
 
@@ -104,23 +97,24 @@ export default class A3mMSA extends BaseMSA {
       return false
     }
 
-    const rows = seqs.map(parseRow)
-    const hasLowercase = rows.some(r => r.inserts.some(i => !!i))
-    const sameMatchLength = new Set(rows.map(r => r.matches.length)).size === 1
-
-    return hasLowercase && sameMatchLength
-  }
-
-  getMSA() {
-    return this.MSA
-  }
-
-  getNames() {
-    return this.orderedNames
-  }
-
-  getRow(name: string) {
-    return this.MSA.seqdata[name] ?? ''
+    let hasLowercase = false
+    let matchCount: number | undefined
+    for (const seq of seqs) {
+      let matches = 0
+      for (let i = 0; i < seq.length; i++) {
+        const code = seq.charCodeAt(i)
+        if (isMatch(code)) {
+          matches++
+        } else if (isLower(code)) {
+          hasLowercase = true
+        }
+      }
+      if (matchCount !== undefined && matches !== matchCount) {
+        return false
+      }
+      matchCount = matches
+    }
+    return hasLowercase
   }
 }
 
@@ -129,7 +123,7 @@ export default class A3mMSA extends BaseMSA {
  * the longest insert any row places there, and rows without one are padded with
  * '.' so all rows stay in register.
  */
-function expandA3M(rawSeqs: string[], names: string[]): Record<string, string> {
+function expandA3M(rawSeqs: string[]): string[] {
   const rows = rawSeqs.map(parseRow)
   // a loop, not Math.max(...): an a3m from an hhblits search routinely carries
   // six figures of hits, and spreading one argument per row throws
@@ -147,9 +141,7 @@ function expandA3M(rawSeqs: string[], names: string[]): Record<string, string> {
     }
   }
 
-  const expanded: Record<string, string> = Object.create(null)
-
-  for (const [seqIdx, { matches, inserts }] of rows.entries()) {
+  return rows.map(({ matches, inserts }) => {
     const result: string[] = []
     for (let pos = 0; pos <= numPositions; pos++) {
       const ins = inserts[pos] ?? ''
@@ -159,8 +151,6 @@ function expandA3M(rawSeqs: string[], names: string[]): Record<string, string> {
         result.push(matches[pos] ?? '-')
       }
     }
-    expanded[names[seqIdx]!] = result.join('')
-  }
-
-  return expanded
+    return result.join('')
+  })
 }

package/src/msa/BaseMSA.ts

@@ -1,12 +1,31 @@
 import type { MSATrack, NodeWithIds } from '../types.ts'
 
 export default abstract class BaseMSA {
-  abstract getMSA(): unknown
-  abstract getRow(name: string): string
-  abstract getNames(): string[]
-
+  protected rows = new Map<string, string>()
+  private names: string[]
   private width?: number
 
+  /**
+   * A repeated name keeps its first row: names index the rows, so listing the
+   * name twice would render a phantom duplicate row.
+   */
+  constructor(rows: Iterable<readonly [string, string]>) {
+    for (const [name, seq] of rows) {
+      if (!this.rows.has(name)) {
+        this.rows.set(name, seq)
+      }
+    }
+    this.names = [...this.rows.keys()]
+  }
+
+  getRow(name: string): string {
+    return this.rows.get(name) ?? ''
+  }
+
+  getNames(): string[] {
+    return this.names
+  }
+
   /**
    * 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

package/src/msa/ClustalMSA.ts

@@ -5,40 +5,16 @@ import BaseMSA from './BaseMSA.ts'
 export default class ClustalMSA extends BaseMSA {
   private MSA: ReturnType<typeof parse>
 
-  // getRow is called once per leaf on every render pass, so a linear scan of
-  // alns makes a full pass quadratic in the row count
-  private byName: Map<string, string>
-
   constructor(text: string) {
-    super()
-    this.MSA = parse(text)
-    this.byName = new Map()
-    for (const aln of this.MSA.alns) {
-      // first wins, as the find() this replaced did
-      if (!this.byName.has(aln.id)) {
-        this.byName.set(aln.id, aln.seq)
-      }
-    }
-  }
-
-  getMSA() {
-    return this.MSA
-  }
-
-  getRow(name: string): string {
-    return this.byName.get(name) ?? ''
+    const msa = parse(text)
+    super(msa.alns.map(aln => [aln.id, aln.seq]))
+    this.MSA = msa
   }
 
   getHeader() {
     return this.MSA.header
   }
 
-  // deduped, matching the first-wins byName map: emitting a repeated id twice
-  // renders a phantom duplicate row showing the first record's residues
-  getNames() {
-    return [...this.byName.keys()]
-  }
-
   get seqConsensus() {
     return this.MSA.consensus
   }

package/src/msa/EmfMSA.ts

@@ -3,35 +3,7 @@ import { parseEmfAln } from 'emf-js'
 import BaseMSA from './BaseMSA.ts'
 
 export default class EmfMSA extends BaseMSA {
-  private MSA: ReturnType<typeof parseEmfAln>
-
-  // getRow is called once per leaf on every render pass, so a linear scan of
-  // the alignment makes a full pass quadratic in the row count
-  private byName: Map<string, string>
-
   constructor(text: string) {
-    super()
-    this.MSA = parseEmfAln(text)
-    this.byName = new Map()
-    for (const aln of this.MSA) {
-      // first wins, as the find() this replaced did
-      if (!this.byName.has(aln.protein)) {
-        this.byName.set(aln.protein, aln.seq)
-      }
-    }
-  }
-
-  getMSA() {
-    return this.MSA
-  }
-
-  getRow(name: string): string {
-    return this.byName.get(name) ?? ''
-  }
-
-  // deduped, matching the first-wins byName map: emitting a repeated id twice
-  // renders a phantom duplicate row showing the first record's residues
-  getNames() {
-    return [...this.byName.keys()]
+    super(parseEmfAln(text).map(aln => [aln.protein, aln.seq]))
   }
 }