trying to reconcile with fix for 33

nathandunn commented 3 years ago

fixes https://github.com/GMOD/apollo-gmod-js/issues/33

Fix this in FeatureService (maybe a unit test? )

[x] fix CDS return string (the CDS may not be coded in the right position)?
[x] in FeatureService, calculate type properly instead of using transcript.instanceOf(MRNA.class)
[x] StopCodonReadThrough stopCodonReadThrough = cdsService.createStopCodonReadThrough(cds);
[x] cdsService.setStopCodonReadThrough(cds, stopCodonReadThrough);
[x] clean out

Maybe need to do a create with Cypher here

nathandunn commented 3 years ago

This almost works (stop codon read through gets set), but the CDS is starting in the wrong position:


# expected protein
MESAIVHLEQSVQKADGKLDMIAWQIDAFEKEFEDPGSEISVLRLLRSVHQVTKDYQNLRQEILEVQQLQKQLSDSLKAQLSQVHGHFNLLRNKIVGQNKNLQLK

# expected cDNA
GCTTTTCAAATATGCCAGTGAGAGCATATCGATTCTAGTGTAAGAAAGTTAACCAACGACTTCACACGAACGGTTTGTGAGTTACGTTTTCTTCGTTTAAAATAATCTGTTACAAATAATAGATAATATGGAATCTGCTATTGTTCATCTTGAACAAAGCGTGCAAAAGGCTGATGGAAAACTAGACATGATTGCATGGCAAATTGATGCTTTTGAAAAAGAATTTGAAGATCCTGGTAGTGAGATTTCTGTGCTTCGTCTATTACGGTCTGTTCATCAAGTCACAAAAGATTATCAGAACCTTCGGCAAGAAATATTGGAGGTTCAACAATTGCAAAAGCAACTTTCAGATTCCCTTAAAGCACAATTATCTCAAGTGCATGGACATTTTAACTTATTACGCAATAAAATAGTAGGACAAAATAAAAATCTACAATTAAAATAAGATTAAAATTTTTTATTTATATTTAAAGTATAATTTAAATATATTTTTTAAATTATACTTAATTTATAATTTTTTATTATAAAATTATTATTAATATTTTAAATCAAAAGTTATTAAAATAACA

# expected CDS (734734 - 735446)
ATGGAATCTGCTATTGTTCATCTTGAACAAAGCGTGCAAAAGGCTGATGGAAAACTAGACATGATTGCATGGCAAATTGATGCTTTTGAAAAAGAATTTGAAGATCCTGGTAGTGAGATTTCTGTGCTTCGTCTATTACGGTCTGTTCATCAAGTCACAAAAGATTATCAGAACCTTCGGCAAGAAATATTGGAGGTTCAACAATTGCAAAAGCAACTTTCAGATTCCCTTAAAGCACAATTATCTCAAGTGCATGGACATTTTAACTTATTACGCAATAAAATAGTAGGACAAAATAAAAATCTACAATTAAAATAA

# actual CDS (loses the first 33 bp).  (734733 - 735446)
GTGCAAAAGGCTGATGGAAAACTAGACATGATTGCATGGCAAATTGATGCTTTTGAAAAAGAATTTGAAGATCCTGGTAGTGAGATTTCTGTGCTTCGTCTATTACGGTCTGTTCATCAAGTCACAAAAGATTATCAGAACCTTCGGCAAGAAATATTGGAGGTTCAACAATTGCAAAAGCAACTTTCAGATTCCCTTAAAGCACAATTATCTCAAGTGCATGGACATTTTAACTTATTACGCAATAAAATAGTAGGACAAAATAAAAATCTACAATTAAAATAA

# the CDS is correct, but there is an issue with the residues . . wonder if its missing an exon

# expected genomics (734608 - ~73570)
GCTTTTCAAATATGCCAGTGAGAGCATATCGATTCTAGTGTAAGAAAGTTAACCAACGACTTCACACGAACGGTTTGTGAGTTACGTTTTCTTCGTTTAAAATAATCTGTTACAAATAATAGATAATATGGAATCTGCTATTGTTCATCTTGAACAAAGCGTAAGTATTTTTATTAGTTTTTATTCATTTTCGGATTGTTCATTTTGAATGTTATTTATGTTTTTCAATAACTATTAAATCTATATTGAATTCAAGCGAATGTCAAATGCTATTTTATTATATAAATAATAAATTAATATTTTATAAATTATTGAATGTTATAGGTGCAAAAGGCTGATGGAAAACTAGACATGATTGCATGGCAAATTGATGCTTTTGAAAAAGAATTTGAAGATCCTGGTAGTGAGGTATGTTTTGTTTAAGAAAATATGACTTATATATTTTTTATTAATTGTTTATTAAATAAAATTCATAGATAGTTAGCAAAAAATTATATTTTTCTTTAAATGTCAATTGTTAAATTAATAGGAAAAAATTTAGTTAGAAAAAATTATAATTCAACTTATTTGCTTAAAGGGTATCAAATTTAAAATTTAAATTGCTATTTTTATTTTTATTCTTTTTTATGCTTTTAACAGATTTCTGTGCTTCGTCTATTACGGTCTGTTCATCAAGTCACAAAAGATTATCAGAACCTTCGGCAAGAAATATTGGAGGTTCAACAATTGCAAAAGCAACTTTCAGATTCCCTTAAAGCACAATTATCTCAAGTGCATGGACATTTTAACTTATTACGCAATAAAATAGTAGGACAAAATAAAAATCTACAATTAAAATAAGATTAAAATTTTTTATTTATATTTAAAGTATAATTTAAATATATTTTTTAAATTATACTTAATTTATAATTTTTTATTATAAAATTATTATTAATATTTTAAATCAAAAGTTATTAAAATAACA

nathandunn commented 3 years ago

From group1.10 honeybee

GMOD / Apollo3Server

trying to reconcile with fix for 33 #81