@apollo-annotation/mst 0.3.4 → 0.3.6

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/mst",
-  "version": "0.3.4",
+  "version": "0.3.6",
   "main": "./dist/index.js",
   "scripts": {
     "build": "tsc"

package/src/AnnotationFeatureModel.ts

@@ -1,10 +1,10 @@
 import { getSession, intersection2 } from '@jbrowse/core/util'
 import {
-  IAnyModelType,
-  IMSTMap,
-  Instance,
-  SnapshotIn,
-  SnapshotOrInstance,
+  type IAnyModelType,
+  type IMSTMap,
+  type Instance,
+  type SnapshotIn,
+  type SnapshotOrInstance,
   cast,
   getParentOfType,
   getSnapshot,
@@ -23,7 +23,7 @@ export interface TranscriptPartLocation {
 }
 
 export interface TranscriptPartNonCoding extends TranscriptPartLocation {
-  type: 'fivePrimeUTR' | 'threePrimeUTR' | 'intron'
+  type: 'fivePrimeUTR' | 'threePrimeUTR' | 'intron' | 'exon'
 }
 
 export interface TranscriptPartCoding extends TranscriptPartLocation {
@@ -126,6 +126,56 @@ export const AnnotationFeatureModel = types
       }
       return false
     },
+    get transcriptExonParts(): TranscriptParts {
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-explicit-any
+      const session = getSession(self) as any
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
+      const { apolloDataStore } = session
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-unsafe-member-access
+      const { featureTypeOntology } = apolloDataStore.ontologyManager
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+      if (!featureTypeOntology.isTypeOf(self.type, 'transcript')) {
+        throw new Error(
+          'Feature is not a transcript or equivalent, cannot calculate exon locations',
+        )
+      }
+      const children = self.children as Children
+      if (!children) {
+        throw new Error('No exons in transcript')
+      }
+      const sortedChildren = [...children.values()]
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+        .filter((child) => featureTypeOntology.isTypeOf(child.type, 'exon'))
+        .sort((a, b) => a.min - b.min)
+      let lastMax = self.min
+      const parts: TranscriptParts = []
+      for (const child of sortedChildren) {
+        if (child.min > lastMax) {
+          parts.push({
+            min: lastMax,
+            max: child.min,
+            type: 'intron',
+          })
+        }
+        parts.push({
+          min: child.min,
+          max: child.max,
+          type: 'exon',
+        })
+        lastMax = child.max
+      }
+      if (lastMax < self.max) {
+        parts.push({
+          min: lastMax,
+          max: self.max,
+          type: 'intron',
+        })
+      }
+      if (self.strand === -1) {
+        parts.reverse()
+      }
+      return parts
+    },
     get transcriptParts(): TranscriptParts[] {
       // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-explicit-any
       const session = getSession(self) as any
@@ -147,10 +197,11 @@ export const AnnotationFeatureModel = types
         // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
         (child) => featureTypeOntology.isTypeOf(child.type, 'CDS'),
       )
+      const transcriptParts: TranscriptParts[] = []
       if (cdsChildren.length === 0) {
-        throw new Error('no CDS in transcript')
+        transcriptParts.push(this.transcriptExonParts)
+        return transcriptParts
       }
-      const transcriptParts: TranscriptParts[] = []
       for (const cds of cdsChildren) {
         const { max: cdsMax, min: cdsMin } = cds
         const parts: TranscriptParts = []
@@ -240,6 +291,48 @@ export const AnnotationFeatureModel = types
         transcript.filter((transcriptPart) => transcriptPart.type === 'CDS'),
       )
     },
+    get looksLikeGene(): boolean {
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-explicit-any
+      const session = getSession(self) as any
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
+      const { apolloDataStore } = session
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-unsafe-member-access
+      const { featureTypeOntology } = apolloDataStore.ontologyManager
+      if (!featureTypeOntology) {
+        return false
+      }
+      const children = self.children as Children
+      if (!children?.size) {
+        return false
+      }
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
+      const isGene =
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+        featureTypeOntology.isTypeOf(self.type, 'gene') ||
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+        featureTypeOntology.isTypeOf(self.type, 'pseudogene')
+      if (!isGene) {
+        return false
+      }
+      for (const [, child] of children) {
+        if (
+          // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+          featureTypeOntology.isTypeOf(child.type, 'transcript') ||
+          // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+          featureTypeOntology.isTypeOf(child.type, 'pseudogenic_transcript')
+        ) {
+          const { children: grandChildren } = child
+          if (!grandChildren?.size) {
+            return false
+          }
+          return [...grandChildren.values()].some((grandchild) =>
+            // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+            featureTypeOntology.isTypeOf(grandchild.type, 'exon'),
+          )
+        }
+      }
+      return false
+    },
   }))
   .actions((self) => ({
     setAttributes(attributes: Map<string, string[]>) {

package/src/ApolloAssembly.ts

@@ -1,4 +1,4 @@
-import { Instance, SnapshotIn, types } from 'mobx-state-tree'
+import { type Instance, type SnapshotIn, types } from 'mobx-state-tree'
 
 import { ApolloRefSeq } from './ApolloRefSeq'
 

package/src/ApolloRefSeq.ts

@@ -1,14 +1,14 @@
 import { isContainedWithin } from '@jbrowse/core/util'
 import {
-  Instance,
-  SnapshotIn,
-  SnapshotOrInstance,
+  type Instance,
+  type SnapshotIn,
+  type SnapshotOrInstance,
   types,
 } from 'mobx-state-tree'
 
 import {
   AnnotationFeatureModel,
-  AnnotationFeatureSnapshot,
+  type AnnotationFeatureSnapshot,
 } from './AnnotationFeatureModel'
 
 export const Sequence = types.model({
@@ -43,7 +43,9 @@ export const ApolloRefSeq = types
     },
     addSequence(seq: SnapshotOrInstance<typeof Sequence>) {
       if (seq.sequence.length !== seq.stop - seq.start) {
-        throw new Error('sequence does not match declared length')
+        throw new Error(
+          `sequence does not match declared length: ${JSON.stringify(seq)}`,
+        )
       }
       if (self.sequence.length === 0) {
         self.sequence.push(seq)
@@ -59,7 +61,13 @@ export const ApolloRefSeq = types
         stop: seq.stop,
         sequence: seq.sequence,
       })
-      newSequences.sort((s1, s2) => s1.start - s2.start)
+      newSequences.sort((s1, s2) => {
+        if (s1.start === s2.start) {
+          return s1.stop - s2.stop
+        }
+        return s1.start - s2.start
+      })
+
       // eslint-disable-next-line unicorn/no-array-reduce
       const consolidatedSequences = newSequences.reduce<SequenceSnapshot[]>(
         (result, current) => {
@@ -69,10 +77,9 @@ export const ApolloRefSeq = types
           }
           if (lastRange.stop >= current.start) {
             if (current.stop > lastRange.stop) {
+              const overlapLength = lastRange.stop - current.start
               lastRange.stop = current.stop
-              lastRange.sequence += current.sequence.slice(
-                current.stop - lastRange.stop,
-              )
+              lastRange.sequence += current.sequence.slice(overlapLength)
             }
           } else {
             result.push(current)
@@ -81,6 +88,13 @@ export const ApolloRefSeq = types
         },
         [],
       )
+      for (const seq of consolidatedSequences) {
+        if (seq.sequence.length !== seq.stop - seq.start) {
+          throw new Error(
+            'Consolidated sequence does not match declared length',
+          )
+        }
+      }
       if (
         self.sequence.length === consolidatedSequences.length &&
         self.sequence.every(

package/src/CheckResult.ts

@@ -1,10 +1,11 @@
-import { Instance, SnapshotIn, types } from 'mobx-state-tree'
+import { type Instance, type SnapshotIn, types } from 'mobx-state-tree'
 
 import { AnnotationFeatureModel } from './AnnotationFeatureModel'
 
 export const CheckResult = types.model('CheckResult', {
   _id: types.identifier,
   name: types.string,
+  cause: types.string,
   ids: types.array(types.safeReference(AnnotationFeatureModel)),
   refSeq: types.string,
   start: types.number,