Weird workaround

GMOD · Nov 6, 2024 · 0605413 · 0605413
1 parent 9c925b7
commit 0605413
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Showing 2 changed files with 66 additions and 2 deletions.
diff --git a/plugins/bed/src/BigBedAdapter/BigBedAdapter.ts b/plugins/bed/src/BigBedAdapter/BigBedAdapter.ts
@@ -21,6 +21,7 @@ import { Observer } from 'rxjs'
 import {
   isUcscProcessedTranscript,
   ucscProcessedTranscript,
+  makeRepeatTrackDescription,
   makeBlocks,
   arrayify,
 } from '../util'
@@ -154,6 +155,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
         chrom,
         chromStart,
         chromEnd,
+        description,
         chromStarts: chromStarts2,
         blockStarts: blockStarts2,
         blockSizes: blockSizes2,
@@ -184,6 +186,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
           strand,
           blockCount,
           thickStart,
+          description,
         })
       ) {
         const f = ucscProcessedTranscript({
@@ -195,6 +198,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
           end: feat.end,
           refName: query.refName,
           score,
+          description,
           chromStarts: chromStarts!,
           blockSizes: blockSizes!,
           blockCount,
@@ -214,7 +218,10 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             )
           ) {
             observer.next(
-              new SimpleFeature({ id: `${this.id}-${uniqueId}`, data: f }),
+              new SimpleFeature({
+                id: `${this.id}-${uniqueId}`,
+                data: f,
+              }),
             )
           }
         }
@@ -232,6 +239,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
               id: `${this.id}-${uniqueId}`,
               data: {
                 ...rest,
+                ...makeRepeatTrackDescription(description),
                 start: feat.start,
                 end: feat.end,
                 strand,

diff --git a/plugins/bed/src/util.ts b/plugins/bed/src/util.ts
@@ -19,6 +19,8 @@ export interface TranscriptFeat extends MinimalFeature {
   subfeatures: MinimalFeature[]
 }
 
+const SPECIFIC_LENGTH_OF_REPEAT_MASKER_DESCRIPTION_FIELDS = 15
+
 export function ucscProcessedTranscript(feature: TranscriptFeat) {
   const {
     subfeatures: oldSubfeatures,
@@ -219,6 +221,7 @@ export function featureData(
     thickStart,
     thickEnd,
     type,
+    description,
     strand: strand2,
     score: score2,
     chrom: _1,
@@ -243,6 +246,7 @@ export function featureData(
 
   const f = {
     ...rest,
+    ...makeRepeatTrackDescription(description),
     type,
     score,
     start,
@@ -266,6 +270,7 @@ export function featureData(
       strand,
       blockCount,
       thickStart,
+      description,
     })
       ? ucscProcessedTranscript({
           thickStart: thickStart!,
@@ -283,12 +288,20 @@ export function isUcscProcessedTranscript({
   thickStart,
   blockCount,
   strand,
+  description,
 }: {
   thickStart?: number
   blockCount?: number
   strand?: number
+  description?: string
 }) {
-  return thickStart && blockCount && strand !== 0
+  return (
+    thickStart &&
+    blockCount &&
+    strand !== 0 &&
+    description?.trim().split(' ').length !==
+      SPECIFIC_LENGTH_OF_REPEAT_MASKER_DESCRIPTION_FIELDS
+  )
 }
 
 export function arrayify(f?: string | number[]) {
@@ -298,3 +311,46 @@ export function arrayify(f?: string | number[]) {
       : f
     : undefined
 }
+
+export function makeRepeatTrackDescription(description?: string) {
+  if (
+    description?.trim().split(' ').length ===
+    SPECIFIC_LENGTH_OF_REPEAT_MASKER_DESCRIPTION_FIELDS
+  ) {
+    const [
+      bitsw_score,
+      percent_div,
+      percent_del,
+      percent_ins,
+      query_chr,
+      query_begin,
+      query_end,
+      query_remaining,
+      orientation,
+      matching_repeat_name,
+      matching_repeat_class,
+      matching_repeat_begin,
+      matching_repeat_end,
+      matching_repeat_remaining,
+      repeat_id,
+    ] = description.trim().split(' ')
+    return {
+      bitsw_score,
+      percent_div,
+      percent_del,
+      percent_ins,
+      query_chr,
+      query_begin,
+      query_end,
+      query_remaining,
+      orientation,
+      matching_repeat_name,
+      matching_repeat_class,
+      matching_repeat_begin,
+      matching_repeat_end,
+      matching_repeat_remaining,
+      repeat_id,
+    }
+  }
+  return { description }
+}