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Add mashmap PAF support #2670

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merged 2 commits into from
Jan 24, 2022
Merged

Add mashmap PAF support #2670

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e2a4224
Allow space-separated PAF from mashmap
cmdcolin Jan 24, 2022
a2c6166
Add mashmap
cmdcolin Jan 24, 2022
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2 changes: 1 addition & 1 deletion plugins/dotplot-view/src/DotplotView/components/ImportForm.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,7 @@ const DotplotImportForm = observer(({ model }: { model: DotplotViewModel }) => {
</a>{' '}
file for the dotplot view. Note that the first assembly should be
the left column of the PAF and the second assembly should be the
right column
right column. PAF-like files from MashMap (.out) are also allowed
</p>
<Grid container justifyContent="center">
<Grid item>
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21 changes: 12 additions & 9 deletions plugins/dotplot-view/src/PAFAdapter/PAFAdapter.ts
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Expand Up @@ -61,9 +61,14 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
encoding: 'utf8',
...opts,
})
const pafRecords: PafRecord[] = []
text.split('\n').forEach((line: string, index: number) => {
if (line.length) {

// mashmap produces PAF-like data that is space separated instead of tab
const hasTab = text.indexOf('\t')
const splitChar = hasTab !== -1 ? '\t' : ' '
return text
.split('\n')
.filter(line => !!line)
.map(line => {
const [
chr1,
,
Expand All @@ -78,7 +83,7 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
blockLen,
mappingQual,
...fields
] = line.split('\t')
] = line.split(splitChar)

const rest = Object.fromEntries(
fields.map(field => {
Expand All @@ -89,7 +94,7 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
}),
)

pafRecords[index] = {
return {
records: [
{ refName: chr1, start: +start1, end: +end1 },
{ refName: chr2, start: +start2, end: +end2 },
Expand All @@ -101,10 +106,8 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
mappingQual: +mappingQual,
...rest,
},
}
}
})
return pafRecords
} as PafRecord
})
}

async hasDataForRefName() {
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3 changes: 2 additions & 1 deletion plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -137,7 +137,8 @@ const ImportForm = observer(({ model }: { model: LinearSyntenyViewModel }) => {
</a>{' '}
file for the linear synteny view. Note that the first assembly
should be the left column of the PAF and the second assembly should
be the right column
be the right column. PAF-like files from MashMap (.out) are also
allowed
</Typography>
<Grid item>
<FileSelector
Expand Down