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Merge pull request #72 from manulera/issue_71
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closes #71
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@tnrich
tnrich authored May 10, 2024
2 parents a782652 + 8a3fe76 commit 66234b3
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Showing 2 changed files with 140 additions and 43 deletions.
137 changes: 94 additions & 43 deletions packages/bio-parsers/src/genbankToJson.js
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,40 @@ import splitStringIntoLines from "./utils/splitStringIntoLines.js";

import createInitialSequence from "./utils/createInitialSequence";

function wrapOriginSpanningFeatures(
locArrayInput,
sequenceLength,
inclusive1BasedStart,
inclusive1BasedEnd
) {
// In genbank files, locations of origin-spanning features are represented as follows:
// complement(join(490883..490885,1..879)) (for a circular sequence of length 490885)
// Then, for locations in locArray we check if there is a location that ends at sequenceLength
// joined with a location that starts at 1. If so, we merge them into a single location.
// (see https://github.com/TeselaGen/tg-oss/issues/35)

// make a deep copy of the array to avoid modifying the original
const locArrayOutput = locArrayInput.map(loc => ({ ...loc }));

// Iterate by pairs of features
for (let i = 0; i < locArrayOutput.length - 1; i++) {
const firstFeature = locArrayOutput[i];
const secondFeature = locArrayOutput[i + 1];
if (
firstFeature.end === sequenceLength - (inclusive1BasedEnd ? 0 : 1) &&
secondFeature.start === 1 - (inclusive1BasedStart ? 0 : 1)
) {
// Merge the two features
locArrayOutput[i] = {
start: firstFeature.start,
end: secondFeature.end
};
locArrayOutput.splice(i + 1, 1);
}
}
return locArrayOutput;
}

export function parseFeatureLocation(
locStr,
isProtein,
Expand All @@ -17,22 +51,37 @@ export function parseFeatureLocation(
sequenceLength
) {
locStr = locStr.trim();
const locArr = [];
locStr.replace(/(\d+)/g, function (string, match) {
locArr.push(match);
const positionsArray = [];
// Genbank feature locations can be:
// 4 -> single base (equivalent to 4..4)
// 4..8 -> range
// complement(4..8) -> complement of range
// join(4..8, 10..12) -> join of ranges
// complement(join(4..8, 10..12)) -> complement of join of ranges
// but also
// join(4, 10..12) -> join of single base and range
// First we split with commas to obtain pairs of positions
const locationParts = locStr.split(",");
locationParts.forEach(locPart => {
// Extract two integers from loc, if only one is present
// we push the same one as the end (e.g. if location is `4` we push
// 4 twice
const extractedPositions = locPart.match(/(\d+)/g);
// Sometimes the location is split between two lines and has a trailing comma
if (extractedPositions === null) {
return;
}
positionsArray.push(extractedPositions[0]);
positionsArray.push(extractedPositions[1] || extractedPositions[0]);
});

const locArray = [];
for (let i = 0; i < locArr.length; i += 2) {
const start = parseInt(locArr[i], 10) - (inclusive1BasedStart ? 0 : 1);
let end = parseInt(locArr[i + 1], 10) - (inclusive1BasedEnd ? 0 : 1);
if (isNaN(end)) {
//if no end is supplied, assume that the end should be set to whatever the start is
//this makes a feature location passed as:
//147
//function like:
//147..147
end = start;
}
for (let i = 0; i < positionsArray.length; i += 2) {
const start =
parseInt(positionsArray[i], 10) - (inclusive1BasedStart ? 0 : 1);
const end =
parseInt(positionsArray[i + 1], 10) - (inclusive1BasedEnd ? 0 : 1);

const location = {
start: start,
end: end
Expand All @@ -41,31 +90,21 @@ export function parseFeatureLocation(
isProtein ? convertAACaretPositionOrRangeToDna(location) : location
);
}
// In genbank files, origin-spanning features are represented as follows:
// complement(join(490883..490885,1..879)) (for a circular sequence of length 490885)
// Then, for locations in locArray we check if there is a feature that ends at sequenceLength
// joined with a feature that starts at 1. If so, we merge them into a single feature.
// (see https://github.com/TeselaGen/tg-oss/issues/35)

if (isCircular) {
// Iterate by pairs of features
for (let i = 0; i < locArray.length; i += 2) {
const firstFeature = locArray[i];
const secondFeature = locArray[i + 1];
if (
firstFeature.end === sequenceLength - (inclusive1BasedEnd ? 0 : 1) &&
secondFeature.start === 1 - (inclusive1BasedStart ? 0 : 1)
) {
// Merge the two features
locArray[i] = {
start: firstFeature.start,
end: secondFeature.end
};
locArray.splice(i + 1, 1);
}
}
// sequenceLength will not be set when this is called during genbank parsing,
// and the wrapping is done in endSeq > postProcessCurSeq > postProcessGenbankFeature
// However, this is useful if the function is used as a standalone parser of
// feature locations.
if (isCircular && sequenceLength) {
return wrapOriginSpanningFeatures(
locArray,
sequenceLength,
inclusive1BasedStart,
inclusive1BasedEnd
);
} else {
return locArray;
}
return locArray;
}

function genbankToJson(string, options = {}) {
Expand Down Expand Up @@ -182,7 +221,7 @@ function genbankToJson(string, options = {}) {
parseOrigin(line, key);
break;
case genbankAnnotationKey.END_SEQUENCE_TAG:
endSeq();
endSeq(options);
break;
case genbankAnnotationKey.DEFINITION_TAG:
line = line.replace(/DEFINITION/, "");
Expand Down Expand Up @@ -321,10 +360,10 @@ function genbankToJson(string, options = {}) {

return results;

function endSeq() {
function endSeq(options) {
//do some post processing clean-up
hasFoundLocus = false;
postProcessCurSeq();
postProcessCurSeq(options);
//push the result into the resultsArray
resultsArray.push(result || { success: false });
}
Expand All @@ -341,11 +380,13 @@ function genbankToJson(string, options = {}) {
}
}

function postProcessCurSeq() {
function postProcessCurSeq(options) {
if (result && result.parsedSequence && result.parsedSequence.features) {
for (let i = 0; i < result.parsedSequence.features.length; i++) {
result.parsedSequence.features[i] = postProcessGenbankFeature(
result.parsedSequence.features[i]
result.parsedSequence.features[i],
result.parsedSequence,
options
);
}
}
Expand Down Expand Up @@ -656,7 +697,7 @@ function genbankToJson(string, options = {}) {
return runon;
}

function postProcessGenbankFeature(feat) {
function postProcessGenbankFeature(feat, parsedSequence, options) {
if (feat.notes.label) {
feat.name = feat.notes.label[0];
} else if (feat.notes.gene) {
Expand Down Expand Up @@ -697,6 +738,16 @@ function genbankToJson(string, options = {}) {
: undefined;
delete feat.notes.direction;
}
if (parsedSequence.circular) {
const { inclusive1BasedStart, inclusive1BasedEnd } = options;
feat.locations = wrapOriginSpanningFeatures(
feat.locations,
parsedSequence.sequence.length,
inclusive1BasedStart,
inclusive1BasedEnd
);
}

return feat;
}
}
Expand Down
46 changes: 46 additions & 0 deletions packages/bio-parsers/test/genbankToJson.test.js
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Original file line number Diff line number Diff line change
Expand Up @@ -1042,6 +1042,21 @@ ORIGIN
{ start: 2, end: 3 }
]
},
// Single position location in join
{
input: "complement(join(1,3..4))",
output: [
{ start: 0, end: 0 },
{ start: 2, end: 3 }
]
},
{
input: "complement(join(1..2,3))",
output: [
{ start: 0, end: 1 },
{ start: 2, end: 2 }
]
},
// Origin-spanning features
{
input: "complement(join(3..4,1..2))",
Expand All @@ -1057,6 +1072,37 @@ ORIGIN
expect(result).toEqual(output);
});
});
it("correctly parses origin-spanning features in genbank files", () => {
const str = `LOCUS . 20 bp DNA circular UNK 01-JAN-1980
DEFINITION .
ACCESSION <unknown id>
VERSION <unknown id>
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
misc_feature join(19..20,1)
ORIGIN
1 aaaaaaaaaa aaaaaaaaaa
//
`;
const result = genbankToJson(str);

expect(result[0].parsedSequence.features[0].locations).toEqual(
undefined,
"origin-spanning locations should have been merged"
);
expect(result[0].parsedSequence.features[0].start).toEqual(
18,
"start should be 18"
);
expect(result[0].parsedSequence.features[0].end).toEqual(
0,
"end should be 0"
);
});
});

// const string = fs.readFileSync(path.join(__dirname, '../../../..', './testData/genbank (JBEI Private)/46.gb'), "utf8");
Expand Down

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