msa-parsers 7.0.0 → 8.1.0

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Files changed (16) hide show
  1. package/README.md +4 -4
  2. package/dist/gff/gffToAnnotations.js +33 -0
  3. package/dist/gff/gffToAnnotations.js.map +1 -1
  4. package/dist/msa/BaseMSA.d.ts +3 -7
  5. package/dist/msa/BaseMSA.js +3 -7
  6. package/dist/msa/BaseMSA.js.map +1 -1
  7. package/dist/msa/stockholmParser.js +3 -0
  8. package/dist/msa/stockholmParser.js.map +1 -1
  9. package/dist/types.d.ts +7 -0
  10. package/package.json +3 -3
  11. package/src/gff/gffToAnnotations.test.ts +34 -0
  12. package/src/gff/gffToAnnotations.ts +39 -0
  13. package/src/msa/BaseMSA.ts +3 -7
  14. package/src/msa/stockholmParser.test.ts +11 -0
  15. package/src/msa/stockholmParser.ts +3 -0
  16. package/src/types.ts +7 -0
package/README.md CHANGED
@@ -30,9 +30,9 @@ pnpm add msa-parsers
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30
 
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  ### Parsing MSA files
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- `parseMSA` sniffs the format from the content, not from the file name. Pass a
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- format as the third argument to settle it yourself -- FASTA and A3M share a
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- leading `>`, so auto-detection between them is a heuristic:
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+ `parseMSA` sniffs the format from the content, not from the file name. FASTA and
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+ A3M share a leading `>`, so telling them apart is heuristic; pass a format as
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+ the third argument to override the guess:
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  ```typescript
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  import { parseMSA } from 'msa-parsers'
@@ -77,7 +77,7 @@ const treeWithIds = generateNodeIds(tree)
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  Every source of overlay annotations converts to one flat list of `Annotation` (a
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  row name, an accession, a name, a description and a 1-based inclusive interval),
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- and that list is what the viewer draws.
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+ and the viewer draws that list.
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  ```typescript
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  import {
package/dist/gff/gffToAnnotations.js CHANGED
@@ -22,6 +22,37 @@ function geneStrand({ type, strand }) {
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  const directional = strand === '+' ? 1 : strand === '-' ? -1 : undefined;
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  return GENE_LEVEL_TYPES.has(type) ? directional : undefined;
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  }
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+ // The nine columns a feature line holds; every other key of a record came from
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+ // column 9
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+ const GFF_COLUMNS = new Set([
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+ 'seq_id',
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+ 'source',
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+ 'type',
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+ 'start',
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+ 'end',
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+ 'score',
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+ 'strand',
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+ 'phase',
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+ ]);
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+ function attributesOf(record) {
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+ const entries = Object.entries(record).filter(([key, value]) => !GFF_COLUMNS.has(key) && typeof value === 'string');
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+ return entries.length > 0 ? Object.fromEntries(entries) : undefined;
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+ }
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+ // JBrowse and IGV read an RGB triple as well as a named or hex color, and the
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+ // attribute parser has already turned `255,0,0` into `255 0 0` by splitting on
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+ // the GFF3 multi-value comma
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+ const RGB_TRIPLE = /^(\d{1,3})[\s,]+(\d{1,3})[\s,]+(\d{1,3})$/;
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+ function cssColor(record) {
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+ const value = (record.color ??
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+ record.colour ??
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+ record.Color ??
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+ record.Colour);
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+ if (!value) {
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+ return undefined;
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+ }
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+ const triple = RGB_TRIPLE.exec(value.trim());
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+ return triple ? `rgb(${triple[1]},${triple[2]},${triple[3]})` : value.trim();
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+ }
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  // InterProScan describes the sequence it scanned before listing the matches
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  // against it. Those lines span the whole row and carry no signature, so they
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  // would draw a full-width block labelled by an md5.
@@ -58,6 +89,8 @@ export function gffToAnnotations(gffRecords) {
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  start: record.start,
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  end: record.end,
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  strand: geneStrand(record),
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+ color: cssColor(record),
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+ attributes: attributesOf(record),
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  };
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  });
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  }
package/dist/gff/gffToAnnotations.js.map CHANGED
@@ -1 +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,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;SAC3B,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}
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,+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/msa/BaseMSA.d.ts CHANGED
@@ -5,13 +5,9 @@ export default abstract class BaseMSA {
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5
  abstract getNames(): string[];
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  private width?;
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  /**
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- * Column count of the alignment: the length of its widest row.
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- *
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- * Not the first row's length. Ragged input is real -- a hand-edited fasta, or
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- * an aligner that stops a row at its last residue -- and taking row 0 makes
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- * every column past it unreachable when row 0 is the short one. The viewer's
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- * gap analysis already defines the column count this way, so anything else
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- * disagrees with it.
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+ * Column count of the alignment: the length of its widest row, since a
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+ * hand-edited fasta or some aligners leave rows short. The viewer's gap
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+ * analysis counts columns the same way.
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  */
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  getWidth(): number;
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  getTree(): NodeWithIds;
package/dist/msa/BaseMSA.js CHANGED
@@ -1,13 +1,9 @@
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  export default class BaseMSA {
2
2
  width;
3
3
  /**
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- * Column count of the alignment: the length of its widest row.
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- *
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- * Not the first row's length. Ragged input is real -- a hand-edited fasta, or
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- * an aligner that stops a row at its last residue -- and taking row 0 makes
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- * every column past it unreachable when row 0 is the short one. The viewer's
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- * gap analysis already defines the column count this way, so anything else
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- * disagrees with it.
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+ * Column count of the alignment: the length of its widest row, since a
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+ * hand-edited fasta or some aligners leave rows short. The viewer's gap
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+ * analysis counts columns the same way.
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  */
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  getWidth() {
13
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  this.width ??= this.getNames().reduce((max, name) => Math.max(max, this.getRow(name).length), 0);
package/dist/msa/BaseMSA.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"BaseMSA.js","sourceRoot":"","sources":["../../src/msa/BaseMSA.ts"],"names":[],"mappings":"AAEA,MAAM,CAAC,OAAO,OAAgB,OAAO;IAK3B,KAAK,CAAS;IAEtB;;;;;;;;OAQG;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"}
1
+ {"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/stockholmParser.js CHANGED
@@ -49,6 +49,9 @@ export function parseAll(text, opts) {
49
49
  for (const line of lines) {
50
50
  let match;
51
51
  if (formatStartRegex.test(line)) {
52
+ if (stock) {
53
+ db.push(stock);
54
+ }
52
55
  stock = createStockholm();
53
56
  treeContinues = false;
54
57
  }
package/dist/msa/stockholmParser.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"stockholmParser.js","sourceRoot":"","sources":["../../src/msa/stockholmParser.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAWH,SAAS,eAAe;IACtB,OAAO;QACL,EAAE,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;QACvB,EAAE,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;QACvB,EAAE,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;QACvB,EAAE,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;QACvB,OAAO,EAAE,EAAE;QACX,OAAO,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;KAC7B,CAAA;AACH,CAAC;AAED,yEAAyE;AACzE,kDAAkD;AAClD,SAAS,WAAW,CAClB,KAA2B,EAC3B,MAAe;IAEf,IAAI,KAAK,EAAE,CAAC;QACV,OAAO,KAAK,CAAA;IACd,CAAC;IACD,IAAI,MAAM,EAAE,CAAC;QACX,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAA;IACtD,CAAC;IACD,OAAO,eAAe,EAAE,CAAA;AAC1B,CAAC;AAED,MAAM,gBAAgB,GAAG,kBAAkB,CAAA;AAC3C,MAAM,cAAc,GAAG,WAAW,CAAA;AAClC,MAAM,OAAO,GAAG,2BAA2B,CAAA;AAC3C,MAAM,OAAO,GAAG,2BAA2B,CAAA;AAC3C,MAAM,OAAO,GAAG,mCAAmC,CAAA;AACnD,MAAM,OAAO,GAAG,mCAAmC,CAAA;AACnD,8EAA8E;AAC9E,yEAAyE;AACzE,6EAA6E;AAC7E,MAAM,SAAS,GAAG,6BAA6B,CAAA;AAC/C,MAAM,aAAa,GAAG,IAAI,CAAA;AAE1B,MAAM,UAAU,KAAK,CAAC,IAAY;IAChC,OAAO,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,UAAU,QAAQ,CACtB,IAAY,EACZ,IAA2B;IAE3B,MAAM,OAAO,GAAG,IAAI,IAAI,EAAE,CAAA;IAC1B,MAAM,EAAE,GAAoB,EAAE,CAAA;IAC9B,IAAI,KAAK,GAAyB,IAAI,CAAA;IACtC,wEAAwE;IACxE,6CAA6C;IAC7C,IAAI,aAAa,GAAG,KAAK,CAAA;IAEzB,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC9B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,KAA6B,CAAA;QAEjC,IAAI,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YAChC,KAAK,GAAG,eAAe,EAAE,CAAA;YACzB,aAAa,GAAG,KAAK,CAAA;QACvB,CAAC;aAAM,IAAI,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACrC,IAAI,KAAK,EAAE,CAAC;gBACV,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAChB,CAAC;YACD,KAAK,GAAG,IAAI,CAAA;QACd,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,MAAM,MAAM,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,KAAK,EAAE,CAAC,CAAA;YACrC,IAAI,GAAG,KAAK,IAAI,IAAI,aAAa,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACvD,MAAM,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAE,CAAA;YACxC,CAAC;iBAAM,CAAC;gBACN,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,CAAA;YACxB,CAAC;YACD,aAAa,GAAG,GAAG,KAAK,IAAI,CAAA;QAC9B,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,IAAI,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QAC/D,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,MAAM,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,KAAK,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAC3D;YAAA,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,KAAK,EAAE,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,CAAA;QAC7C,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,MAAM,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,KAAK,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAA;YAC5D,MAAM,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,IAAI,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QAC3D,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YAC1C,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,IAAI,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,KAAK,SAAS,EAAE,CAAC;gBACzC,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;gBAC3B,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YAC7B,CAAC;YACD,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,OAAO,CAAA;QACnC,CAAC;aAAM,IAAI,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACpC,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;gBACnB,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;YACnC,CAAC;QACH,CAAC;IACH,CAAC;IAED,IAAI,KAAK,EAAE,CAAC;QACV,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IAChB,CAAC;IAED,OAAO,EAAE,CAAA;AACX,CAAC;AAED,MAAM,UAAU,KAAK,CACnB,IAAY,EACZ,IAA2B;IAE3B,MAAM,EAAE,GAAG,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;IAC/B,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACpB,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxC,CAAC;IACD,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAClB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;IAClD,CAAC;IACD,OAAO,EAAE,CAAC,CAAC,CAAE,CAAA;AACf,CAAC"}
1
+ {"version":3,"file":"stockholmParser.js","sourceRoot":"","sources":["../../src/msa/stockholmParser.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAWH,SAAS,eAAe;IACtB,OAAO;QACL,EAAE,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;QACvB,EAAE,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;QACvB,EAAE,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;QACvB,EAAE,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;QACvB,OAAO,EAAE,EAAE;QACX,OAAO,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC;KAC7B,CAAA;AACH,CAAC;AAED,yEAAyE;AACzE,kDAAkD;AAClD,SAAS,WAAW,CAClB,KAA2B,EAC3B,MAAe;IAEf,IAAI,KAAK,EAAE,CAAC;QACV,OAAO,KAAK,CAAA;IACd,CAAC;IACD,IAAI,MAAM,EAAE,CAAC;QACX,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAA;IACtD,CAAC;IACD,OAAO,eAAe,EAAE,CAAA;AAC1B,CAAC;AAED,MAAM,gBAAgB,GAAG,kBAAkB,CAAA;AAC3C,MAAM,cAAc,GAAG,WAAW,CAAA;AAClC,MAAM,OAAO,GAAG,2BAA2B,CAAA;AAC3C,MAAM,OAAO,GAAG,2BAA2B,CAAA;AAC3C,MAAM,OAAO,GAAG,mCAAmC,CAAA;AACnD,MAAM,OAAO,GAAG,mCAAmC,CAAA;AACnD,8EAA8E;AAC9E,yEAAyE;AACzE,6EAA6E;AAC7E,MAAM,SAAS,GAAG,6BAA6B,CAAA;AAC/C,MAAM,aAAa,GAAG,IAAI,CAAA;AAE1B,MAAM,UAAU,KAAK,CAAC,IAAY;IAChC,OAAO,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,UAAU,QAAQ,CACtB,IAAY,EACZ,IAA2B;IAE3B,MAAM,OAAO,GAAG,IAAI,IAAI,EAAE,CAAA;IAC1B,MAAM,EAAE,GAAoB,EAAE,CAAA;IAC9B,IAAI,KAAK,GAAyB,IAAI,CAAA;IACtC,wEAAwE;IACxE,6CAA6C;IAC7C,IAAI,aAAa,GAAG,KAAK,CAAA;IAEzB,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC9B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,KAA6B,CAAA;QAEjC,IAAI,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YAChC,IAAI,KAAK,EAAE,CAAC;gBACV,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAChB,CAAC;YACD,KAAK,GAAG,eAAe,EAAE,CAAA;YACzB,aAAa,GAAG,KAAK,CAAA;QACvB,CAAC;aAAM,IAAI,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACrC,IAAI,KAAK,EAAE,CAAC;gBACV,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAChB,CAAC;YACD,KAAK,GAAG,IAAI,CAAA;QACd,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,MAAM,MAAM,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,KAAK,EAAE,CAAC,CAAA;YACrC,IAAI,GAAG,KAAK,IAAI,IAAI,aAAa,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACvD,MAAM,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAE,CAAA;YACxC,CAAC;iBAAM,CAAC;gBACN,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,CAAA;YACxB,CAAC;YACD,aAAa,GAAG,GAAG,KAAK,IAAI,CAAA;QAC9B,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,IAAI,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QAC/D,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,MAAM,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,KAAK,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAC3D;YAAA,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,KAAK,EAAE,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,CAAA;QAC7C,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,MAAM,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,KAAK,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAA;YAC5D,MAAM,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,IAAI,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QAC3D,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YAC1C,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,IAAI,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,KAAK,SAAS,EAAE,CAAC;gBACzC,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;gBAC3B,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YAC7B,CAAC;YACD,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,OAAO,CAAA;QACnC,CAAC;aAAM,IAAI,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACpC,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;gBACnB,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;YACnC,CAAC;QACH,CAAC;IACH,CAAC;IAED,IAAI,KAAK,EAAE,CAAC;QACV,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IAChB,CAAC;IAED,OAAO,EAAE,CAAA;AACX,CAAC;AAED,MAAM,UAAU,KAAK,CACnB,IAAY,EACZ,IAA2B;IAE3B,MAAM,EAAE,GAAG,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;IAC/B,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACpB,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxC,CAAC;IACD,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAClB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;IAClD,CAAC;IACD,OAAO,EAAE,CAAC,CAAC,CAAE,CAAA;AACf,CAAC"}
package/dist/types.d.ts CHANGED
@@ -58,6 +58,13 @@ export interface Annotation {
58
58
  start: number;
59
59
  end: number;
60
60
  strand?: number;
61
+ /**
62
+ * CSS color the feature carries itself, from a GFF3 `color=` attribute. It
63
+ * overrides the palette and any scale a channel resolves.
64
+ */
65
+ color?: string;
66
+ /** the GFF attributes of column 9, for a channel encoding one of them */
67
+ attributes?: Record<string, string>;
61
68
  }
62
69
  /**
63
70
  * One signature hit. `entry` is the InterPro entry the signature is integrated
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "msa-parsers",
3
- "version": "7.0.0",
3
+ "version": "8.1.0",
4
4
  "license": "MIT",
5
5
  "type": "module",
6
6
  "repository": {
@@ -21,7 +21,7 @@
21
21
  ],
22
22
  "dependencies": {
23
23
  "@gmod/newick": "^1.0.3",
24
- "clustal-js": "^2.0.17",
24
+ "clustal-js": "^2.0.18",
25
25
  "emf-js": "^2.0.0"
26
26
  },
27
27
  "publishConfig": {
@@ -29,7 +29,7 @@
29
29
  },
30
30
  "devDependencies": {
31
31
  "typescript": "^7.0.2",
32
- "vitest": "^4.1.10"
32
+ "vitest": "^5.0.0"
33
33
  },
34
34
  "scripts": {
35
35
  "clean": "rimraf dist",
package/src/gff/gffToAnnotations.test.ts CHANGED
@@ -41,6 +41,12 @@ test('maps a record onto the annotation fields', () => {
41
41
  start: 10,
42
42
  end: 50,
43
43
  strand: undefined,
44
+ color: undefined,
45
+ attributes: {
46
+ Name: 'PF00001',
47
+ signature_desc: '7tm_1',
48
+ description: 'GPCR family',
49
+ },
44
50
  },
45
51
  ])
46
52
  })
@@ -104,3 +110,31 @@ test('falls back from Name to ID to source and positions', () => {
104
110
  ]).map(a => a.accession),
105
111
  ).toEqual(['domain_123', 'CustomSource_10_50'])
106
112
  })
113
+
114
+ test('keeps the column 9 attributes, so a channel can encode one of them', () => {
115
+ expect(
116
+ gffToAnnotations([record({ type: 'gene', Name: 'trpB', gene: 'trpB' })])[0]
117
+ ?.attributes,
118
+ ).toEqual({ Name: 'trpB', gene: 'trpB' })
119
+ })
120
+
121
+ test('reads a color attribute under any of its spellings', () => {
122
+ expect(
123
+ gffToAnnotations([
124
+ record({ color: '#ff0000' }),
125
+ record({ colour: 'rebeccapurple' }),
126
+ record({ Color: '#00ff00' }),
127
+ record({ Colour: 'blue' }),
128
+ record({}),
129
+ ]).map(a => a.color),
130
+ ).toEqual(['#ff0000', 'rebeccapurple', '#00ff00', 'blue', undefined])
131
+ })
132
+
133
+ test('normalizes an RGB triple, which the attribute parser hands over space-separated', () => {
134
+ expect(
135
+ gffToAnnotations([
136
+ record({ color: '255 0 0' }),
137
+ record({ color: '0,128,255' }),
138
+ ]).map(a => a.color),
139
+ ).toEqual(['rgb(255,0,0)', 'rgb(0,128,255)'])
140
+ })
package/src/gff/gffToAnnotations.ts CHANGED
@@ -26,6 +26,43 @@ function geneStrand({ type, strand }: GFFRecord): number | undefined {
26
26
  return GENE_LEVEL_TYPES.has(type) ? directional : undefined
27
27
  }
28
28
 
29
+ // The nine columns a feature line holds; every other key of a record came from
30
+ // column 9
31
+ const GFF_COLUMNS = new Set([
32
+ 'seq_id',
33
+ 'source',
34
+ 'type',
35
+ 'start',
36
+ 'end',
37
+ 'score',
38
+ 'strand',
39
+ 'phase',
40
+ ])
41
+
42
+ function attributesOf(record: GFFRecord) {
43
+ const entries = Object.entries(record).filter(
44
+ ([key, value]) => !GFF_COLUMNS.has(key) && typeof value === 'string',
45
+ ) as [string, string][]
46
+ return entries.length > 0 ? Object.fromEntries(entries) : undefined
47
+ }
48
+
49
+ // JBrowse and IGV read an RGB triple as well as a named or hex color, and the
50
+ // attribute parser has already turned `255,0,0` into `255 0 0` by splitting on
51
+ // the GFF3 multi-value comma
52
+ const RGB_TRIPLE = /^(\d{1,3})[\s,]+(\d{1,3})[\s,]+(\d{1,3})$/
53
+
54
+ function cssColor(record: GFFRecord) {
55
+ const value = (record.color ??
56
+ record.colour ??
57
+ record.Color ??
58
+ record.Colour) as string | undefined
59
+ if (!value) {
60
+ return undefined
61
+ }
62
+ const triple = RGB_TRIPLE.exec(value.trim())
63
+ return triple ? `rgb(${triple[1]},${triple[2]},${triple[3]})` : value.trim()
64
+ }
65
+
29
66
  // InterProScan describes the sequence it scanned before listing the matches
30
67
  // against it. Those lines span the whole row and carry no signature, so they
31
68
  // would draw a full-width block labelled by an md5.
@@ -66,6 +103,8 @@ export function gffToAnnotations(gffRecords: GFFRecord[]): Annotation[] {
66
103
  start: record.start,
67
104
  end: record.end,
68
105
  strand: geneStrand(record),
106
+ color: cssColor(record),
107
+ attributes: attributesOf(record),
69
108
  }
70
109
  })
71
110
  }
package/src/msa/BaseMSA.ts CHANGED
@@ -8,13 +8,9 @@ export default abstract class BaseMSA {
8
8
  private width?: number
9
9
 
10
10
  /**
11
- * Column count of the alignment: the length of its widest row.
12
- *
13
- * Not the first row's length. Ragged input is real -- a hand-edited fasta, or
14
- * an aligner that stops a row at its last residue -- and taking row 0 makes
15
- * every column past it unreachable when row 0 is the short one. The viewer's
16
- * gap analysis already defines the column count this way, so anything else
17
- * disagrees with it.
11
+ * Column count of the alignment: the length of its widest row, since a
12
+ * hand-edited fasta or some aligners leave rows short. The viewer's gap
13
+ * analysis counts columns the same way.
18
14
  */
19
15
  getWidth(): number {
20
16
  this.width ??= this.getNames().reduce(
package/src/msa/stockholmParser.test.ts CHANGED
@@ -133,6 +133,17 @@ seq2 GHIKL
133
133
  })
134
134
  })
135
135
 
136
+ test('a header ends the open alignment when its // is missing', () => {
137
+ const db = parseAll(`# STOCKHOLM 1.0
138
+ seq1 ACDEF
139
+ # STOCKHOLM 1.0
140
+ seq2 GHIKL
141
+ //`)
142
+ expect(db).toHaveLength(2)
143
+ expect(db[0]?.seqdata).toEqual({ seq1: 'ACDEF' })
144
+ expect(db[1]?.seqdata).toEqual({ seq2: 'GHIKL' })
145
+ })
146
+
136
147
  test('joins a tree split across #=GF NH lines, starting a new one at TN', () => {
137
148
  const [aln] = parseAll(`# STOCKHOLM 1.0
138
149
  #=GF TN first
package/src/msa/stockholmParser.ts CHANGED
@@ -71,6 +71,9 @@ export function parseAll(
71
71
  let match: RegExpExecArray | null
72
72
 
73
73
  if (formatStartRegex.test(line)) {
74
+ if (stock) {
75
+ db.push(stock)
76
+ }
74
77
  stock = createStockholm()
75
78
  treeContinues = false
76
79
  } else if (formatEndRegex.test(line)) {
package/src/types.ts CHANGED
@@ -64,6 +64,13 @@ export interface Annotation {
64
64
  start: number
65
65
  end: number
66
66
  strand?: number
67
+ /**
68
+ * CSS color the feature carries itself, from a GFF3 `color=` attribute. It
69
+ * overrides the palette and any scale a channel resolves.
70
+ */
71
+ color?: string
72
+ /** the GFF attributes of column 9, for a channel encoding one of them */
73
+ attributes?: Record<string, string>
67
74
  }
68
75
 
69
76
  /**