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support RNA sequence in gb file #5

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merged 7 commits into from
Jul 26, 2023
Merged

support RNA sequence in gb file #5

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62dd54e
support RNA sequence
sunm19810-pki Jul 20, 2023
42aaa83
Merge pull request #1 from PerkinElmer/CLN-54033
sunm19810-pki Jul 24, 2023
510aff8
more changes
sunm19810-pki Jul 24, 2023
92c0168
support export ds-RNA
sunm19810-pki Jul 24, 2023
a352aa7
more change
sunm19810-pki Jul 24, 2023
3bfaa4f
add test
sunm19810-pki Jul 26, 2023
0ac7a56
add test
sunm19810-pki Jul 26, 2023
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6 changes: 5 additions & 1 deletion packages/bio-parsers/src/genbankToJson.js
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Original file line number Diff line number Diff line change
Expand Up @@ -338,7 +338,7 @@ function genbankToJson(string, options = {}) {

if (
j === 4 &&
(item.match(/ds-dna/i) || item.match(/ss-dna/i) || item.match(/dna/i))
(item.match(/ds-dna/i) || item.match(/ss-dna/i) || item.match(/dna/i) || item.match(/rna/i))
) {
if (options.isProtein === undefined) {
options.isProtein = false;
Expand All @@ -347,6 +347,9 @@ function genbankToJson(string, options = {}) {
if (item.match(/ss-dna/i)) {
options.isSingleStrandedDNA = true;
}
if (item.match(/rna/i) && !item.match(/ss-rna/i)) {
options.isDoubleStrandedRNA = true;
}
}

// Division
Expand All @@ -368,6 +371,7 @@ function genbankToJson(string, options = {}) {
result.parsedSequence.gbDivision = gbDivision;
result.parsedSequence.sequenceTypeFromLocus = options.sequenceTypeFromLocus;
result.parsedSequence.isSingleStrandedDNA = options.isSingleStrandedDNA;
result.parsedSequence.isDoubleStrandedRNA = options.isDoubleStrandedRNA;
result.parsedSequence.date = date;
result.parsedSequence.circular = circular;
}
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4 changes: 2 additions & 2 deletions packages/bio-parsers/src/jsonToGenbank.js
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Original file line number Diff line number Diff line change
Expand Up @@ -205,9 +205,9 @@ function createGenbankLocus(serSeq, options) {
if (serSeq.isProtein) {
dnaType = "";
} else if (serSeq.type === "RNA") {
dnaType = "RNA";
dnaType = serSeq?.doubleStranded ? 'RNA' : serSeq?.sequenceTypeFromLocus ?? "ss-RNA";
} else {
dnaType = serSeq?.sequenceTypeFromLocus ?? "DNA";
dnaType = serSeq?.doubleStranded ? 'DNA' : serSeq?.sequenceTypeFromLocus ?? "DNA";
}
const date = getCurrentDateString();

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2 changes: 1 addition & 1 deletion packages/sequence-utils/src/getComplementSequenceAndAnnotations.js
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Expand Up @@ -14,7 +14,7 @@ export default function getComplementSequenceAndAnnotations(
options
);
const newSeqObj = Object.assign({}, seqObj, {
sequence: getComplementSequenceString(seqObj.sequence)
sequence: getComplementSequenceString(seqObj.sequence, seqObj.isRna)
});
return tidyUpSequenceData(newSeqObj, options);
};
6 changes: 4 additions & 2 deletions packages/sequence-utils/src/getComplementSequenceString.js
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Original file line number Diff line number Diff line change
@@ -1,12 +1,14 @@
import DNAComplementMap from "./DNAComplementMap";
import { merge } from "lodash";


// ac.throw([ac.string,ac.bool],arguments);
export default function getComplementSequenceString(sequence) {
export default function getComplementSequenceString(sequence, isRna) {
// ac.throw([ac.string],arguments);
let complementSeqString = "";
const complementMap = merge(DNAComplementMap, isRna ? { a: 'u', A: 'U'} : {a: 't', A: 'T'});
for (let i = 0; i < sequence.length; i++) {
let complementChar = DNAComplementMap[sequence[i]];
let complementChar = complementMap[sequence[i]];
if (!complementChar) {
complementChar = sequence[i];
// throw new Error('trying to get the reverse compelement of an invalid base');
Expand Down