p2s_mapper 1.2.1 → 1.2.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/dbIds.js +5 -1
- package/dist/dbIds.js.map +1 -1
- package/dist/uniProtSearch.js +6 -1
- package/dist/uniProtSearch.js.map +1 -1
- package/esm/dbIds.js +5 -1
- package/esm/dbIds.js.map +1 -1
- package/esm/uniProtSearch.js +6 -1
- package/esm/uniProtSearch.js.map +1 -1
- package/package.json +1 -1
- package/src/dbIds.ts +5 -1
- package/src/uniProtSearch.ts +6 -1
package/dist/dbIds.js
CHANGED
|
@@ -11,7 +11,11 @@ const DB_ID_PATTERNS = [
|
|
|
11
11
|
{ db: 'ensembl', pattern: /^ENS[A-Z]*P\d+/i, label: 'Ensembl protein' },
|
|
12
12
|
{ db: 'refseq', pattern: /^[NX]M_\d+/i, label: 'RefSeq mRNA' },
|
|
13
13
|
{ db: 'refseq', pattern: /^[NX]R_\d+/i, label: 'RefSeq ncRNA' },
|
|
14
|
-
|
|
14
|
+
// YP_ and AP_ are the proteins of organelle, viral and prokaryotic genomes.
|
|
15
|
+
// WP_ is left out on purpose: it names one sequence shared by every strain
|
|
16
|
+
// and species that encodes it, so its cross-references are a list of
|
|
17
|
+
// organisms rather than an entry (E. coli's WP_000135199 has six reviewed).
|
|
18
|
+
{ db: 'refseq', pattern: /^[NXYA]P_\d+/i, label: 'RefSeq protein' },
|
|
15
19
|
{ db: 'ccds', pattern: /^CCDS\d+/i, label: 'CCDS' },
|
|
16
20
|
{ db: 'hgnc', pattern: /^HGNC:\d+/i, label: 'HGNC' },
|
|
17
21
|
];
|
package/dist/dbIds.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"dbIds.js","sourceRoot":"","sources":["../src/dbIds.ts"],"names":[],"mappings":";;
|
|
1
|
+
{"version":3,"file":"dbIds.js","sourceRoot":"","sources":["../src/dbIds.ts"],"names":[],"mappings":";;AAsBA,4CAEC;AAGD,wDAEC;AAID,oCAGC;AAID,sDAKC;AAED,oDAEC;AA1CD,MAAM,cAAc,GAAqD;IACvE,EAAE,EAAE,EAAE,SAAS,EAAE,OAAO,EAAE,iBAAiB,EAAE,KAAK,EAAE,cAAc,EAAE;IACpE,EAAE,EAAE,EAAE,SAAS,EAAE,OAAO,EAAE,iBAAiB,EAAE,KAAK,EAAE,oBAAoB,EAAE;IAC1E,EAAE,EAAE,EAAE,SAAS,EAAE,OAAO,EAAE,iBAAiB,EAAE,KAAK,EAAE,iBAAiB,EAAE;IACvE,EAAE,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,aAAa,EAAE;IAC9D,EAAE,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,cAAc,EAAE;IAC/D,4EAA4E;IAC5E,2EAA2E;IAC3E,qEAAqE;IACrE,4EAA4E;IAC5E,EAAE,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,eAAe,EAAE,KAAK,EAAE,gBAAgB,EAAE;IACnE,EAAE,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,WAAW,EAAE,KAAK,EAAE,MAAM,EAAE;IACnD,EAAE,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,KAAK,EAAE,MAAM,EAAE;CACrD,CAAA;AAED,SAAgB,gBAAgB,CAAC,EAAU;IACzC,OAAO,cAAc,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAA;AACrD,CAAC;AAED,8DAA8D;AAC9D,SAAgB,sBAAsB,CAAC,EAAU;IAC/C,OAAO,gBAAgB,CAAC,EAAE,CAAC,KAAK,SAAS,CAAA;AAC3C,CAAC;AAED;8CAC8C;AAC9C,SAAgB,YAAY,CAAC,EAAU;IACrC,MAAM,KAAK,GAAG,gBAAgB,CAAC,EAAE,CAAC,CAAA;IAClC,OAAO,KAAK,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,EAAE,CAAA;AAC9C,CAAC;AAED;4EAC4E;AAC5E,SAAgB,qBAAqB,CAAC,EAAU;IAC9C,MAAM,KAAK,GAAG,gBAAgB,CAAC,EAAE,CAAC,CAAA;IAClC,OAAO,KAAK;QACV,CAAC,CAAC,QAAQ,KAAK,CAAC,EAAE,IAAI,KAAK,CAAC,EAAE,KAAK,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE;QAC1E,CAAC,CAAC,SAAS,CAAA;AACf,CAAC;AAED,SAAgB,oBAAoB,CAAC,CAAU;IAC7C,OAAO,CAAC,EAAE,OAAO,CAAC,WAAW,EAAE,EAAE,CAAC,CAAA;AACpC,CAAC"}
|
package/dist/uniProtSearch.js
CHANGED
|
@@ -63,8 +63,13 @@ async function searchByGeneName(geneName, organismId, opts) {
|
|
|
63
63
|
// are 284812. The descendants are asked only on a miss, because for a
|
|
64
64
|
// species with reviewed subspecies entries (human and Neanderthal) they
|
|
65
65
|
// turn one answer into two.
|
|
66
|
+
// The taxon itself has answered, so the wider question failing leaves
|
|
67
|
+
// that answer standing rather than turning an empty result into an error.
|
|
66
68
|
const entries = exact.length === 0 && organismId
|
|
67
|
-
? await searchUniProt(buildGeneNameQuery(geneName, organismId, 'taxonomy_id'), 5, opts)
|
|
69
|
+
? await searchUniProt(buildGeneNameQuery(geneName, organismId, 'taxonomy_id'), 5, opts).catch((e) => {
|
|
70
|
+
console.error(`descendant-taxon search failed for ${geneName}:`, e);
|
|
71
|
+
return exact;
|
|
72
|
+
})
|
|
68
73
|
: exact;
|
|
69
74
|
return { entries, error: undefined };
|
|
70
75
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"uniProtSearch.js","sourceRoot":"","sources":["../src/uniProtSearch.ts"],"names":[],"mappings":";;AAmFA,gDAYC;
|
|
1
|
+
{"version":3,"file":"uniProtSearch.js","sourceRoot":"","sources":["../src/uniProtSearch.ts"],"names":[],"mappings":";;AAmFA,gDAYC;AA6ED,oDAgEC;AA5OD,mDAA2C;AAC3C,yCAImB;AAsCnB,MAAM,cAAc,GAClB,6DAA6D,CAAA;AAE/D,SAAS,mBAAmB,CAC1B,MAAsC;IAEtC,OAAO;QACL,SAAS,EAAE,MAAM,CAAC,gBAAgB;QAClC,EAAE,EAAE,MAAM,CAAC,WAAW;QACtB,QAAQ,EAAE,MAAM,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,KAAK;QAC5C,YAAY,EACV,MAAM,CAAC,QAAQ,EAAE,UAAU,IAAI,MAAM,CAAC,QAAQ,EAAE,cAAc;QAChE,WAAW,EAAE,MAAM,CAAC,kBAAkB,EAAE,eAAe,EAAE,QAAQ,EAAE,KAAK;QACxE,UAAU,EAAE,MAAM,CAAC,SAAS,KAAK,iCAAiC;KACnE,CAAA;AACH,CAAC;AAED,KAAK,UAAU,aAAa,CAC1B,KAAa,EACb,IAAY,EACZ,IAAmB;IAEnB,MAAM,GAAG,GAAG,mDAAmD,kBAAkB,CAAC,KAAK,CAAC,WAAW,cAAc,SAAS,IAAI,EAAE,CAAA;IAChI,MAAM,IAAI,GAAG,MAAM,IAAA,yBAAS,EAAmB,GAAG,EAAE,IAAI,CAAC,CAAA;IACzD,OAAO,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,mBAAmB,CAAC,CAAA;AAC9C,CAAC;AAED;;;;;;;;;;;;GAYG;AACH,SAAgB,kBAAkB,CAChC,QAAgB,EAChB,UAAmB,EACnB,QAAuC,aAAa;IAEpD,OAAO;QACL,eAAe,QAAQ,CAAC,UAAU,CAAC,GAAG,EAAE,KAAK,CAAC,GAAG;QACjD,UAAU,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,UAAU,EAAE,CAAC,CAAC,CAAC,SAAS;QACjD,eAAe;KAChB;SACE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,SAAS,CAAC;SAC5B,IAAI,CAAC,OAAO,CAAC,CAAA;AAClB,CAAC;AAOD,KAAK,UAAU,YAAY,CACzB,EAAU,EACV,IAAmB;IAEnB,MAAM,KAAK,GAAG,IAAA,gCAAqB,EAAC,EAAE,CAAC,CAAA;IACvC,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,CAAA;IAC1C,CAAC;IACD,IAAI,CAAC;QACH,OAAO,EAAE,OAAO,EAAE,MAAM,aAAa,CAAC,KAAK,EAAE,EAAE,EAAE,IAAI,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,CAAA;IAC5E,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO,CAAC,KAAK,CAAC,0BAA0B,EAAE,GAAG,EAAE,CAAC,CAAC,CAAA;QACjD,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAA;IAClC,CAAC;AACH,CAAC;AAED,KAAK,UAAU,gBAAgB,CAC7B,QAAgB,EAChB,UAA8B,EAC9B,IAAmB;IAEnB,IAAI,CAAC;QACH,MAAM,KAAK,GAAG,MAAM,aAAa,CAC/B,kBAAkB,CAAC,QAAQ,EAAE,UAAU,CAAC,EACxC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,EACnB,IAAI,CACL,CAAA;QACD,0EAA0E;QAC1E,0EAA0E;QAC1E,sEAAsE;QACtE,wEAAwE;QACxE,4BAA4B;QAC5B,sEAAsE;QACtE,0EAA0E;QAC1E,MAAM,OAAO,GACX,KAAK,CAAC,MAAM,KAAK,CAAC,IAAI,UAAU;YAC9B,CAAC,CAAC,MAAM,aAAa,CACjB,kBAAkB,CAAC,QAAQ,EAAE,UAAU,EAAE,aAAa,CAAC,EACvD,CAAC,EACD,IAAI,CACL,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACrB,OAAO,CAAC,KAAK,CAAC,sCAAsC,QAAQ,GAAG,EAAE,CAAC,CAAC,CAAA;gBACnE,OAAO,KAAK,CAAA;YACd,CAAC,CAAC;YACJ,CAAC,CAAC,KAAK,CAAA;QACX,OAAO,EAAE,OAAO,EAAE,KAAK,EAAE,SAAS,EAAE,CAAA;IACtC,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO,CAAC,KAAK,CAAC,+BAA+B,QAAQ,GAAG,EAAE,CAAC,CAAC,CAAA;QAC5D,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAA;IAClC,CAAC;AACH,CAAC;AAED,SAAS,kBAAkB,CAAC,OAAuB;IACjD,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAA;IAC9B,MAAM,MAAM,GAAmB,EAAE,CAAA;IACjC,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE,CAAC;QAC5B,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,CAAC;YAC/B,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,CAAA;YACzB,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QACpB,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAQM,KAAK,UAAU,oBAAoB,CACxC,EACE,aAAa,GAAG,EAAE,EAClB,MAAM,EACN,QAAQ,EACR,UAAU,GAOX,EACD,IAAmB;IAEnB,MAAM,WAAW,GAAG,IAAI,GAAG,CAAC,aAAa,CAAC,CAAA;IAC1C,MAAM,cAAc,GAAG,MAAM,CAAC,CAAC,CAAC,IAAA,+BAAoB,EAAC,MAAM,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACxE,IAAI,cAAc,IAAI,IAAA,iCAAsB,EAAC,cAAc,CAAC,EAAE,CAAC;QAC7D,WAAW,CAAC,GAAG,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAED,6EAA6E;IAC7E,2EAA2E;IAC3E,uEAAuE;IACvE,MAAM,CAAC,WAAW,EAAE,UAAU,CAAC,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC;QAClD,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC,YAAY,CAAC,EAAE,EAAE,IAAI,CAAC,CAAC,CAAC;QAC/D,QAAQ,CAAC,CAAC,CAAC,gBAAgB,CAAC,QAAQ,EAAE,UAAU,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,SAAS;KACpE,CAAC,CAAA;IAEF,IAAI,OAAO,GAAG,kBAAkB,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAA;IACrE,wEAAwE;IACxE,6EAA6E;IAC7E,yEAAyE;IACzE,MAAM,mBAAmB,GACvB,UAAU,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAA;IACzE,IAAI,mBAAmB,EAAE,CAAC;QACxB,OAAO,GAAG,kBAAkB,CAAC,CAAC,GAAG,OAAO,EAAE,GAAG,mBAAmB,CAAC,OAAO,CAAC,CAAC,CAAA;IAC5E,CAAC;IAED,MAAM,cAAc,GAAG,WAAW,CAAC,IAAI,GAAG,CAAC,mBAAmB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACvE,MAAM,WAAW,GACf,WAAW,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,CAAC,CAAC,MAAM;QACrD,CAAC,mBAAmB,EAAE,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAEpD,4EAA4E;IAC5E,6EAA6E;IAC7E,IACE,OAAO,CAAC,MAAM,KAAK,CAAC;QACpB,cAAc,GAAG,CAAC;QAClB,cAAc,KAAK,WAAW,EAC9B,CAAC;QACD,MAAM,CACJ,mBAAmB,EAAE,KAAK;YAC1B,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,CAAC,EAAE,KAAK,CACpD,CAAA;IACH,CAAC;IAED,OAAO;QACL,OAAO,EAAE,OAAO,CAAC,QAAQ,CACvB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,CACtD;QACD,cAAc;QACd,WAAW;KACZ,CAAA;AACH,CAAC"}
|
package/esm/dbIds.js
CHANGED
|
@@ -4,7 +4,11 @@ const DB_ID_PATTERNS = [
|
|
|
4
4
|
{ db: 'ensembl', pattern: /^ENS[A-Z]*P\d+/i, label: 'Ensembl protein' },
|
|
5
5
|
{ db: 'refseq', pattern: /^[NX]M_\d+/i, label: 'RefSeq mRNA' },
|
|
6
6
|
{ db: 'refseq', pattern: /^[NX]R_\d+/i, label: 'RefSeq ncRNA' },
|
|
7
|
-
|
|
7
|
+
// YP_ and AP_ are the proteins of organelle, viral and prokaryotic genomes.
|
|
8
|
+
// WP_ is left out on purpose: it names one sequence shared by every strain
|
|
9
|
+
// and species that encodes it, so its cross-references are a list of
|
|
10
|
+
// organisms rather than an entry (E. coli's WP_000135199 has six reviewed).
|
|
11
|
+
{ db: 'refseq', pattern: /^[NXYA]P_\d+/i, label: 'RefSeq protein' },
|
|
8
12
|
{ db: 'ccds', pattern: /^CCDS\d+/i, label: 'CCDS' },
|
|
9
13
|
{ db: 'hgnc', pattern: /^HGNC:\d+/i, label: 'HGNC' },
|
|
10
14
|
];
|
package/esm/dbIds.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"dbIds.js","sourceRoot":"","sources":["../src/dbIds.ts"],"names":[],"mappings":"AAOA,MAAM,cAAc,GAAqD;IACvE,EAAE,EAAE,EAAE,SAAS,EAAE,OAAO,EAAE,iBAAiB,EAAE,KAAK,EAAE,cAAc,EAAE;IACpE,EAAE,EAAE,EAAE,SAAS,EAAE,OAAO,EAAE,iBAAiB,EAAE,KAAK,EAAE,oBAAoB,EAAE;IAC1E,EAAE,EAAE,EAAE,SAAS,EAAE,OAAO,EAAE,iBAAiB,EAAE,KAAK,EAAE,iBAAiB,EAAE;IACvE,EAAE,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,aAAa,EAAE;IAC9D,EAAE,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,cAAc,EAAE;IAC/D,EAAE,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,
|
|
1
|
+
{"version":3,"file":"dbIds.js","sourceRoot":"","sources":["../src/dbIds.ts"],"names":[],"mappings":"AAOA,MAAM,cAAc,GAAqD;IACvE,EAAE,EAAE,EAAE,SAAS,EAAE,OAAO,EAAE,iBAAiB,EAAE,KAAK,EAAE,cAAc,EAAE;IACpE,EAAE,EAAE,EAAE,SAAS,EAAE,OAAO,EAAE,iBAAiB,EAAE,KAAK,EAAE,oBAAoB,EAAE;IAC1E,EAAE,EAAE,EAAE,SAAS,EAAE,OAAO,EAAE,iBAAiB,EAAE,KAAK,EAAE,iBAAiB,EAAE;IACvE,EAAE,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,aAAa,EAAE;IAC9D,EAAE,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,cAAc,EAAE;IAC/D,4EAA4E;IAC5E,2EAA2E;IAC3E,qEAAqE;IACrE,4EAA4E;IAC5E,EAAE,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,eAAe,EAAE,KAAK,EAAE,gBAAgB,EAAE;IACnE,EAAE,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,WAAW,EAAE,KAAK,EAAE,MAAM,EAAE;IACnD,EAAE,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,KAAK,EAAE,MAAM,EAAE;CACrD,CAAA;AAED,MAAM,UAAU,gBAAgB,CAAC,EAAU;IACzC,OAAO,cAAc,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAA;AACrD,CAAC;AAED,8DAA8D;AAC9D,MAAM,UAAU,sBAAsB,CAAC,EAAU;IAC/C,OAAO,gBAAgB,CAAC,EAAE,CAAC,KAAK,SAAS,CAAA;AAC3C,CAAC;AAED;8CAC8C;AAC9C,MAAM,UAAU,YAAY,CAAC,EAAU;IACrC,MAAM,KAAK,GAAG,gBAAgB,CAAC,EAAE,CAAC,CAAA;IAClC,OAAO,KAAK,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,EAAE,CAAA;AAC9C,CAAC;AAED;4EAC4E;AAC5E,MAAM,UAAU,qBAAqB,CAAC,EAAU;IAC9C,MAAM,KAAK,GAAG,gBAAgB,CAAC,EAAE,CAAC,CAAA;IAClC,OAAO,KAAK;QACV,CAAC,CAAC,QAAQ,KAAK,CAAC,EAAE,IAAI,KAAK,CAAC,EAAE,KAAK,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE;QAC1E,CAAC,CAAC,SAAS,CAAA;AACf,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,CAAU;IAC7C,OAAO,CAAC,EAAE,OAAO,CAAC,WAAW,EAAE,EAAE,CAAC,CAAA;AACpC,CAAC"}
|
package/esm/uniProtSearch.js
CHANGED
|
@@ -59,8 +59,13 @@ async function searchByGeneName(geneName, organismId, opts) {
|
|
|
59
59
|
// are 284812. The descendants are asked only on a miss, because for a
|
|
60
60
|
// species with reviewed subspecies entries (human and Neanderthal) they
|
|
61
61
|
// turn one answer into two.
|
|
62
|
+
// The taxon itself has answered, so the wider question failing leaves
|
|
63
|
+
// that answer standing rather than turning an empty result into an error.
|
|
62
64
|
const entries = exact.length === 0 && organismId
|
|
63
|
-
? await searchUniProt(buildGeneNameQuery(geneName, organismId, 'taxonomy_id'), 5, opts)
|
|
65
|
+
? await searchUniProt(buildGeneNameQuery(geneName, organismId, 'taxonomy_id'), 5, opts).catch((e) => {
|
|
66
|
+
console.error(`descendant-taxon search failed for ${geneName}:`, e);
|
|
67
|
+
return exact;
|
|
68
|
+
})
|
|
64
69
|
: exact;
|
|
65
70
|
return { entries, error: undefined };
|
|
66
71
|
}
|
package/esm/uniProtSearch.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"uniProtSearch.js","sourceRoot":"","sources":["../src/uniProtSearch.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC3C,OAAO,EACL,qBAAqB,EACrB,sBAAsB,EACtB,oBAAoB,GACrB,MAAM,YAAY,CAAA;AAsCnB,MAAM,cAAc,GAClB,6DAA6D,CAAA;AAE/D,SAAS,mBAAmB,CAC1B,MAAsC;IAEtC,OAAO;QACL,SAAS,EAAE,MAAM,CAAC,gBAAgB;QAClC,EAAE,EAAE,MAAM,CAAC,WAAW;QACtB,QAAQ,EAAE,MAAM,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,KAAK;QAC5C,YAAY,EACV,MAAM,CAAC,QAAQ,EAAE,UAAU,IAAI,MAAM,CAAC,QAAQ,EAAE,cAAc;QAChE,WAAW,EAAE,MAAM,CAAC,kBAAkB,EAAE,eAAe,EAAE,QAAQ,EAAE,KAAK;QACxE,UAAU,EAAE,MAAM,CAAC,SAAS,KAAK,iCAAiC;KACnE,CAAA;AACH,CAAC;AAED,KAAK,UAAU,aAAa,CAC1B,KAAa,EACb,IAAY,EACZ,IAAmB;IAEnB,MAAM,GAAG,GAAG,mDAAmD,kBAAkB,CAAC,KAAK,CAAC,WAAW,cAAc,SAAS,IAAI,EAAE,CAAA;IAChI,MAAM,IAAI,GAAG,MAAM,SAAS,CAAmB,GAAG,EAAE,IAAI,CAAC,CAAA;IACzD,OAAO,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,mBAAmB,CAAC,CAAA;AAC9C,CAAC;AAED;;;;;;;;;;;;GAYG;AACH,MAAM,UAAU,kBAAkB,CAChC,QAAgB,EAChB,UAAmB,EACnB,QAAuC,aAAa;IAEpD,OAAO;QACL,eAAe,QAAQ,CAAC,UAAU,CAAC,GAAG,EAAE,KAAK,CAAC,GAAG;QACjD,UAAU,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,UAAU,EAAE,CAAC,CAAC,CAAC,SAAS;QACjD,eAAe;KAChB;SACE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,SAAS,CAAC;SAC5B,IAAI,CAAC,OAAO,CAAC,CAAA;AAClB,CAAC;AAOD,KAAK,UAAU,YAAY,CACzB,EAAU,EACV,IAAmB;IAEnB,MAAM,KAAK,GAAG,qBAAqB,CAAC,EAAE,CAAC,CAAA;IACvC,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,CAAA;IAC1C,CAAC;IACD,IAAI,CAAC;QACH,OAAO,EAAE,OAAO,EAAE,MAAM,aAAa,CAAC,KAAK,EAAE,EAAE,EAAE,IAAI,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,CAAA;IAC5E,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO,CAAC,KAAK,CAAC,0BAA0B,EAAE,GAAG,EAAE,CAAC,CAAC,CAAA;QACjD,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAA;IAClC,CAAC;AACH,CAAC;AAED,KAAK,UAAU,gBAAgB,CAC7B,QAAgB,EAChB,UAA8B,EAC9B,IAAmB;IAEnB,IAAI,CAAC;QACH,MAAM,KAAK,GAAG,MAAM,aAAa,CAC/B,kBAAkB,CAAC,QAAQ,EAAE,UAAU,CAAC,EACxC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,EACnB,IAAI,CACL,CAAA;QACD,0EAA0E;QAC1E,0EAA0E;QAC1E,sEAAsE;QACtE,wEAAwE;QACxE,4BAA4B;QAC5B,MAAM,OAAO,GACX,KAAK,CAAC,MAAM,KAAK,CAAC,IAAI,UAAU;YAC9B,CAAC,CAAC,MAAM,aAAa,CACjB,kBAAkB,CAAC,QAAQ,EAAE,UAAU,EAAE,aAAa,CAAC,EACvD,CAAC,EACD,IAAI,CACL;
|
|
1
|
+
{"version":3,"file":"uniProtSearch.js","sourceRoot":"","sources":["../src/uniProtSearch.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC3C,OAAO,EACL,qBAAqB,EACrB,sBAAsB,EACtB,oBAAoB,GACrB,MAAM,YAAY,CAAA;AAsCnB,MAAM,cAAc,GAClB,6DAA6D,CAAA;AAE/D,SAAS,mBAAmB,CAC1B,MAAsC;IAEtC,OAAO;QACL,SAAS,EAAE,MAAM,CAAC,gBAAgB;QAClC,EAAE,EAAE,MAAM,CAAC,WAAW;QACtB,QAAQ,EAAE,MAAM,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,KAAK;QAC5C,YAAY,EACV,MAAM,CAAC,QAAQ,EAAE,UAAU,IAAI,MAAM,CAAC,QAAQ,EAAE,cAAc;QAChE,WAAW,EAAE,MAAM,CAAC,kBAAkB,EAAE,eAAe,EAAE,QAAQ,EAAE,KAAK;QACxE,UAAU,EAAE,MAAM,CAAC,SAAS,KAAK,iCAAiC;KACnE,CAAA;AACH,CAAC;AAED,KAAK,UAAU,aAAa,CAC1B,KAAa,EACb,IAAY,EACZ,IAAmB;IAEnB,MAAM,GAAG,GAAG,mDAAmD,kBAAkB,CAAC,KAAK,CAAC,WAAW,cAAc,SAAS,IAAI,EAAE,CAAA;IAChI,MAAM,IAAI,GAAG,MAAM,SAAS,CAAmB,GAAG,EAAE,IAAI,CAAC,CAAA;IACzD,OAAO,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,mBAAmB,CAAC,CAAA;AAC9C,CAAC;AAED;;;;;;;;;;;;GAYG;AACH,MAAM,UAAU,kBAAkB,CAChC,QAAgB,EAChB,UAAmB,EACnB,QAAuC,aAAa;IAEpD,OAAO;QACL,eAAe,QAAQ,CAAC,UAAU,CAAC,GAAG,EAAE,KAAK,CAAC,GAAG;QACjD,UAAU,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,UAAU,EAAE,CAAC,CAAC,CAAC,SAAS;QACjD,eAAe;KAChB;SACE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,SAAS,CAAC;SAC5B,IAAI,CAAC,OAAO,CAAC,CAAA;AAClB,CAAC;AAOD,KAAK,UAAU,YAAY,CACzB,EAAU,EACV,IAAmB;IAEnB,MAAM,KAAK,GAAG,qBAAqB,CAAC,EAAE,CAAC,CAAA;IACvC,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,CAAA;IAC1C,CAAC;IACD,IAAI,CAAC;QACH,OAAO,EAAE,OAAO,EAAE,MAAM,aAAa,CAAC,KAAK,EAAE,EAAE,EAAE,IAAI,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,CAAA;IAC5E,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO,CAAC,KAAK,CAAC,0BAA0B,EAAE,GAAG,EAAE,CAAC,CAAC,CAAA;QACjD,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAA;IAClC,CAAC;AACH,CAAC;AAED,KAAK,UAAU,gBAAgB,CAC7B,QAAgB,EAChB,UAA8B,EAC9B,IAAmB;IAEnB,IAAI,CAAC;QACH,MAAM,KAAK,GAAG,MAAM,aAAa,CAC/B,kBAAkB,CAAC,QAAQ,EAAE,UAAU,CAAC,EACxC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,EACnB,IAAI,CACL,CAAA;QACD,0EAA0E;QAC1E,0EAA0E;QAC1E,sEAAsE;QACtE,wEAAwE;QACxE,4BAA4B;QAC5B,sEAAsE;QACtE,0EAA0E;QAC1E,MAAM,OAAO,GACX,KAAK,CAAC,MAAM,KAAK,CAAC,IAAI,UAAU;YAC9B,CAAC,CAAC,MAAM,aAAa,CACjB,kBAAkB,CAAC,QAAQ,EAAE,UAAU,EAAE,aAAa,CAAC,EACvD,CAAC,EACD,IAAI,CACL,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACrB,OAAO,CAAC,KAAK,CAAC,sCAAsC,QAAQ,GAAG,EAAE,CAAC,CAAC,CAAA;gBACnE,OAAO,KAAK,CAAA;YACd,CAAC,CAAC;YACJ,CAAC,CAAC,KAAK,CAAA;QACX,OAAO,EAAE,OAAO,EAAE,KAAK,EAAE,SAAS,EAAE,CAAA;IACtC,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO,CAAC,KAAK,CAAC,+BAA+B,QAAQ,GAAG,EAAE,CAAC,CAAC,CAAA;QAC5D,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAA;IAClC,CAAC;AACH,CAAC;AAED,SAAS,kBAAkB,CAAC,OAAuB;IACjD,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAA;IAC9B,MAAM,MAAM,GAAmB,EAAE,CAAA;IACjC,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE,CAAC;QAC5B,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,CAAC;YAC/B,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,CAAA;YACzB,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QACpB,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAQD,MAAM,CAAC,KAAK,UAAU,oBAAoB,CACxC,EACE,aAAa,GAAG,EAAE,EAClB,MAAM,EACN,QAAQ,EACR,UAAU,GAOX,EACD,IAAmB;IAEnB,MAAM,WAAW,GAAG,IAAI,GAAG,CAAC,aAAa,CAAC,CAAA;IAC1C,MAAM,cAAc,GAAG,MAAM,CAAC,CAAC,CAAC,oBAAoB,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACxE,IAAI,cAAc,IAAI,sBAAsB,CAAC,cAAc,CAAC,EAAE,CAAC;QAC7D,WAAW,CAAC,GAAG,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAED,6EAA6E;IAC7E,2EAA2E;IAC3E,uEAAuE;IACvE,MAAM,CAAC,WAAW,EAAE,UAAU,CAAC,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC;QAClD,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC,YAAY,CAAC,EAAE,EAAE,IAAI,CAAC,CAAC,CAAC;QAC/D,QAAQ,CAAC,CAAC,CAAC,gBAAgB,CAAC,QAAQ,EAAE,UAAU,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,SAAS;KACpE,CAAC,CAAA;IAEF,IAAI,OAAO,GAAG,kBAAkB,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAA;IACrE,wEAAwE;IACxE,6EAA6E;IAC7E,yEAAyE;IACzE,MAAM,mBAAmB,GACvB,UAAU,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAA;IACzE,IAAI,mBAAmB,EAAE,CAAC;QACxB,OAAO,GAAG,kBAAkB,CAAC,CAAC,GAAG,OAAO,EAAE,GAAG,mBAAmB,CAAC,OAAO,CAAC,CAAC,CAAA;IAC5E,CAAC;IAED,MAAM,cAAc,GAAG,WAAW,CAAC,IAAI,GAAG,CAAC,mBAAmB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACvE,MAAM,WAAW,GACf,WAAW,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,CAAC,CAAC,MAAM;QACrD,CAAC,mBAAmB,EAAE,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAEpD,4EAA4E;IAC5E,6EAA6E;IAC7E,IACE,OAAO,CAAC,MAAM,KAAK,CAAC;QACpB,cAAc,GAAG,CAAC;QAClB,cAAc,KAAK,WAAW,EAC9B,CAAC;QACD,MAAM,CACJ,mBAAmB,EAAE,KAAK;YAC1B,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,CAAC,EAAE,KAAK,CACpD,CAAA;IACH,CAAC;IAED,OAAO;QACL,OAAO,EAAE,OAAO,CAAC,QAAQ,CACvB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,CACtD;QACD,cAAc;QACd,WAAW;KACZ,CAAA;AACH,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "p2s_mapper",
|
|
3
3
|
"description": "Map a transcript's translation onto a protein structure: alignment, coordinates, chain choice, SIFTS, and the AlphaFold and PDBe lookups that find the structure",
|
|
4
|
-
"version": "1.2.
|
|
4
|
+
"version": "1.2.2",
|
|
5
5
|
"packageManager": "pnpm@11.15.1",
|
|
6
6
|
"repository": {
|
|
7
7
|
"type": "git",
|
package/src/dbIds.ts
CHANGED
|
@@ -11,7 +11,11 @@ const DB_ID_PATTERNS: { db: DbType; pattern: RegExp; label: string }[] = [
|
|
|
11
11
|
{ db: 'ensembl', pattern: /^ENS[A-Z]*P\d+/i, label: 'Ensembl protein' },
|
|
12
12
|
{ db: 'refseq', pattern: /^[NX]M_\d+/i, label: 'RefSeq mRNA' },
|
|
13
13
|
{ db: 'refseq', pattern: /^[NX]R_\d+/i, label: 'RefSeq ncRNA' },
|
|
14
|
-
|
|
14
|
+
// YP_ and AP_ are the proteins of organelle, viral and prokaryotic genomes.
|
|
15
|
+
// WP_ is left out on purpose: it names one sequence shared by every strain
|
|
16
|
+
// and species that encodes it, so its cross-references are a list of
|
|
17
|
+
// organisms rather than an entry (E. coli's WP_000135199 has six reviewed).
|
|
18
|
+
{ db: 'refseq', pattern: /^[NXYA]P_\d+/i, label: 'RefSeq protein' },
|
|
15
19
|
{ db: 'ccds', pattern: /^CCDS\d+/i, label: 'CCDS' },
|
|
16
20
|
{ db: 'hgnc', pattern: /^HGNC:\d+/i, label: 'HGNC' },
|
|
17
21
|
]
|
package/src/uniProtSearch.ts
CHANGED
|
@@ -132,13 +132,18 @@ async function searchByGeneName(
|
|
|
132
132
|
// are 284812. The descendants are asked only on a miss, because for a
|
|
133
133
|
// species with reviewed subspecies entries (human and Neanderthal) they
|
|
134
134
|
// turn one answer into two.
|
|
135
|
+
// The taxon itself has answered, so the wider question failing leaves
|
|
136
|
+
// that answer standing rather than turning an empty result into an error.
|
|
135
137
|
const entries =
|
|
136
138
|
exact.length === 0 && organismId
|
|
137
139
|
? await searchUniProt(
|
|
138
140
|
buildGeneNameQuery(geneName, organismId, 'taxonomy_id'),
|
|
139
141
|
5,
|
|
140
142
|
opts,
|
|
141
|
-
)
|
|
143
|
+
).catch((e: unknown) => {
|
|
144
|
+
console.error(`descendant-taxon search failed for ${geneName}:`, e)
|
|
145
|
+
return exact
|
|
146
|
+
})
|
|
142
147
|
: exact
|
|
143
148
|
return { entries, error: undefined }
|
|
144
149
|
} catch (e) {
|