Start genbank

GMOD · Feb 7, 2023 · 979e476 · 979e476
1 parent 5096330
commit 979e476
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Showing 3 changed files with 51 additions and 3 deletions.
diff --git a/packages/core/pluggableElementTypes/models/components/SaveTrackData.tsx b/packages/core/pluggableElementTypes/models/components/SaveTrackData.tsx
@@ -3,6 +3,11 @@ import {
   Button,
   DialogActions,
   DialogContent,
+  FormControl,
+  FormControlLabel,
+  FormLabel,
+  Radio,
+  RadioGroup,
   TextField,
   Typography,
 } from '@mui/material'
@@ -19,7 +24,7 @@ import { getConf } from '@jbrowse/core/configuration'
 import { BaseTrackModel } from '@jbrowse/core/pluggableElementTypes'
 
 // locals
-import { stringifyGFF3 } from './util'
+import { stringifyGenbank, stringifyGFF3 } from './util'
 
 const useStyles = makeStyles()({
   root: {
@@ -56,6 +61,8 @@ export default observer(function SaveTrackDataDlg({
   const { classes } = useStyles()
   const [error, setError] = useState<unknown>()
   const [features, setFeatures] = useState<Feature[]>()
+  const [type, setType] = useState('gff3')
+  const options = { gff3: 'GFF3', genbank: 'GenBank' }
 
   useEffect(() => {
     // eslint-disable-next-line @typescript-eslint/no-floating-promises
@@ -73,7 +80,11 @@ export default observer(function SaveTrackDataDlg({
     })()
   }, [model])
 
-  const str = features ? stringifyGFF3(features) : ''
+  const str = features
+    ? type === 'gff3'
+      ? stringifyGFF3(features)
+      : stringifyGenbank(features, {})
+    : ''
 
   return (
     <Dialog maxWidth="xl" open onClose={handleClose} title="Save track data">
@@ -84,6 +95,18 @@ export default observer(function SaveTrackDataDlg({
         ) : !features.length ? (
           <Typography>No features found</Typography>
         ) : null}
+
+        <FormControl>
+          <FormLabel>File type</FormLabel>
+          <RadioGroup
+            value={type}
+            onChange={event => setType(event.target.value)}
+          >
+            {Object.entries(options).map(([key, val]) => (
+              <FormControlLabel value={key} control={<Radio />} label={val} />
+            ))}
+          </RadioGroup>
+        </FormControl>
         <TextField
           variant="outlined"
           multiline

diff --git a/packages/core/pluggableElementTypes/models/components/util.ts b/packages/core/pluggableElementTypes/models/components/util.ts
@@ -73,3 +73,25 @@ export function stringifyGFF3(feats: Feature[]) {
     '\n',
   )
 }
+// LOCUS       Exported                1699 bp DNA     linear   UNA 04-FEB-2023
+// FEATURES             Location/Qualifiers
+//     source          1..1699
+//     CDS             join(428..659,794..1099)
+//     CDS             complement(join(1278..1411,1515..1650))
+// ORIGIN
+//       1 ttaatttgaaatagtttccattttttgataataatgaaaagctgctgaaaaaatggtttggcagttagcaattccaggaattttttcgagataagccataaattttaaaattatggaaattgatttacgtgtgtttttttctaattctaaattttttggtgacgttttccacgttgatttatttatttttcgaacccccctttccctcaaccaaaatagtatttattcttcagtttcaatattgtcaaaaagctcgatgcccgagtattttgaatcttctgcgatttcaattagaagaaatgctgcaggaaacgacgttcaaaaggtaattgaaagcatttagaacatctcataaagatgatgtttcagaacaaagttcaaaattggcttcacagtgtgatcgagcgtctcaagtggtggagtcccggacgatgtcagcagctcttcgtcgagaatgagctcatcgagctatgctacagagctcgtgagcagttctggaaaaacaaagtgaagctagatgtacgtttagcgtatgagggattagcaattcattttctaataatttcagatcgaagctcctgtcaaaatctgtggagacattcacggacagttcgaggacttgatggctctgttcgagttgaatgggtggcctgaagagcataagtaagccgccaatttgaatttggattagtatatgttttcatttcagatatctctttcttggtgattatgttgaccgtggtccattctccattgaagtcatcacactcctcttcacctttcaaatattgatgcctgacaaagtcttccttcttcgaggaaaccacgaaagccgccccgtcaatatgcaatatggattttatctggaatgcaagaagcgctactcagtcgccttgtatgatgcatttcaacttgcattcaattgtatgccactgtgcgctgtcgtgagcaagaagatcatatgtatgcatggaggaatatctgaagatctgattgacttgacgtaagatctttttccaatttccttatgtacttcaacaaccaatttccagacaactcgaaaagattgatcgtccatttgatattccggacattggcgtcatctccgacttgacctgggctgatcccgacgagaaggtcttcggatatgccgattctccacgtggcgcgggacgttctttcggtccgaatgcggtcaagaagttccttcaaatgcacaacctggatctagtcgttcgtgcccatcaggtcgtcatggatggttatgaattctttgcggaccgccaacttgtcacagtcttctcggcaccatcatactgcggacaattcgacaatgctgctgccgtgatgaatgttgacgacaaattgctctgtactttcacaatcttccgcccggatttgaaagttggcgacttcaagaagaaggacaagtgatattttgatttatcgaaataaagcattttttgtaccgtcttgattttcaggttaggctcgaatcacgcgcgcctgcttctcgaccttaaaaatgcctccaggtacaccaggaggcgagcccgctaagcaagaattccagcgccttctcccttctctcccgcttcctgagaatattgatgacataatcggtattctttttgtgtgtgcctgtatccattattcacgcacacaagaacaccaacaagcatgctggttttcttatata
+/// /
+export function stringifyGenbank(
+  feats: Feature[],
+  { name = 'Exported', length = 100 }: { name?: string; length?: number },
+) {
+  const today = new Date()
+  const month = today.toLocaleString('en-US', { month: 'short' }).toUpperCase()
+  const day = today.toLocaleString('en-US', { day: 'numeric' })
+  const year = today.toLocaleString('en-US', { year: 'numeric' })
+  const date = `${day}-${month}-${year}`
+  const l1 = `LOCUS       ${name}     ${length} bp DNA      linear    UNA  ${date}`
+  const l2 = 'FEATURES             Location/Qualifiers'
+  const l3 = `     source          1..${length}`
+  return [l1, l2, l3].join('\n')
+}
diff --git a/packages/core/rpc/methods/CoreSaveFeatureData.ts b/packages/core/rpc/methods/CoreSaveFeatureData.ts
@@ -1,5 +1,8 @@
 /* eslint-disable @typescript-eslint/no-non-null-assertion */
 import { toArray } from 'rxjs/operators'
+import { firstValueFrom } from 'rxjs'
+
+// locals
 import { getAdapter } from '../../data_adapters/dataAdapterCache'
 import RpcMethodType from '../../pluggableElementTypes/RpcMethodType'
 import { RenderArgs } from './util'
@@ -58,7 +61,7 @@ export default class CoreGetFeatures extends RpcMethodType {
       ...opts,
       signal,
     })
-    const r = await ret.pipe(toArray()).toPromise()
+    const r = await firstValueFrom(ret.pipe(toArray()))
     return r.map(f => f.toJSON())
   }
 }