loading yeast data in apollo-performance fails to load mRNAs

GMOD / Apollo3Server

Apollo 3 Server: Grails 4 + Neo4j 3.5 + JB2

BSD 3-Clause "New" or "Revised" License

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loading yeast data in apollo-performance fails to load mRNAs #51

Closed nathandunn closed 3 years ago

nathandunn commented 3 years ago

Should be:

 grep -v ^#  loaded-data/yeast/raw/yeast.gff | cut -f3  | sort | uniq -c 
6913 CDS
7416 exon
   4 five_prime_UTR
7024 gene
6600 mRNA
  18 ncRNA
  12 pseudogene
  12 pseudogenic_transcript
  24 rRNA
   6 snRNA
  77 snoRNA
 299 tRNA
  91 transposable_element

nathandunn commented 3 years ago

MATCH (n:Feature) RETURN count(n),labels(n) limit 15

1|424 | ["Gene", "Feature"]
2 | 299 | ["Feature", "NcRNA", "Transcript", "TRNA"]
3 | 491 | ["Feature", "Exon", "TranscriptRegion"]
4 | 18 | ["Feature", "NcRNA", "Transcript"]
5 | 65 | ["Feature", "TranscriptRegion", "NonCanonicalFivePrimeSpliceSite", "SpliceSite"]
6 | 91 | ["Feature", "TransposableElement"]
7 | 65 | ["Feature", "TranscriptRegion", "SpliceSite", "NonCanonicalThreePrimeSpliceSite"]
8 | 77 | ["Feature", "NcRNA", "Transcript", "SnoRNA"]
9 | 6 | ["Feature", "Transcript", "SnRNA"]
10 | 24 | ["Feature", "NcRNA", "Transcript", "RRNA"]

nathandunn commented 3 years ago

[ ] MRNA (should match)
[x] Pseudoge / Pseudogenic_transcript
[ ] Gene (should match or be very close depending on CDS calculations)

[ ] Exon
[ ] (non-canonical splice sites should exist still)
[ ] CDS (should exist still, but we throw them out)

[x] SnoRNA
[x] RRNA
[x] TRNA
[x] ncRNA
[x] SnRNA
[x] TranspobalElement

nathandunn commented 3 years ago

So, pseudogenes also work, its just that psuedogenic_transcript needs to be cast to transcript in the GFF3. Might be worth expanding this, but unsure (better if they were all just SO types).

nathandunn commented 3 years ago

[ ] fix deleteFeatureAndChildren
[ ] add test for add all yeast
[x] add logging exception for all