as_symbolic_or_explicit_according_to_size - gives different results depending if starts as symbolic or not

[davmlaw]

seq = 'AGACAGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGCACAATCTTGGCTCACTGCAAGCTCCGCCTCCCAGGTTCACACCATTCTCCTGCCTCAGCCTCCCGAGTAGCCGGGACTACAGGCGCCCACCACCACGCCCAGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTAGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCACCCACCTCGGCCTCCCAAAGCACTGGGATTACAGGCATGAGCCACCGCGCCGAGCCCCAAGACCTTTCTTTATTACCAGGGCTTCCACAGACCTGACACATGGTAGTTCCTCAATAAATAATTGCAGAATTACTGAAAAATTTTACTGTTAACTTAGGCAGTGGTAAAACCATTGTTTGGTAGCTCAGAACTCAGCAAGTAAATAGCAACATTTGCTGGAAGAACAGATAGTTTTTCAAATCCAATTCAAGGACTGGGTATGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCGTATCCAGGAGTTCGAGACTAGCCTGACCAACATGGTGAAACTCCGTCTCTACTAAAAATACAAAATTAGCCAGGTGTGGTGGTGGGCACCTGTAATCTCAGCTACTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGTAGGCGGAGGTTGTAGTGAGCTGAGATTGTGCCATTGCTCTCCAGCCTGGGAAACAAGAGCAAAACTCCGTCTCAAAAAAAAAAAAAATCCAATTCAAATGATTATGGAAGTAGTGGAGAAATAAACAGGAAAATGATAAATAATTAAGATAATATATAATATGGCTATATTTTAATCTATTGTTGATATGATTTTCTCTTTTCCCCTTGGGATTAGTATCTATCTCTCTACTGGATATTAATTTGTTATATTTTCTCATTAGAGCAAGTTACTCAGATGGAAAACTGAAAGCCCCTCCTAAACCATGTGCTGGCAATCAAGG'
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In [9]: vc = VariantCoordinate(chrom='NC_060927.1', position=37007425, ref='A', alt=seq)

In [10]: vc.as_internal_symbolic(GenomeBuild.t2tv2())
WARNING ClinGen does not support build T2T-CHM13v2.0
Out[10]: VariantCoordinate(chrom='NC_060927.1', position=37007425, ref='A', alt='<DUP>', svlen=999)

In [11]: vc.as_internal_symbolic(GenomeBuild.t2tv2()).as_symbolic_or_explicit_according_to_size(GenomeBuild.t2tv2())
WARNING ClinGen does not support build T2T-CHM13v2.0
Out[11]: VariantCoordinate(chrom='NC_060927.1', position=37007425, ref='A', alt='AGACAGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGCACAATCTTGGCTCACTGCAAGCTCCGCCTCCCAGGTTCACACCATTCTCCTGCCTCAGCCTCCCGAGTAGCCGGGACTACAGGCGCCCACCACCACGCCCAGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTAGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCACCCACCTCGGCCTCCCAAAGCACTGGGATTACAGGCATGAGCCACCGCGCCGAGCCCCAAGACCTTTCTTTATTACCAGGGCTTCCACAGACCTGACACATGGTAGTTCCTCAATAAATAATTGCAGAATTACTGAAAAATTTTACTGTTAACTTAGGCAGTGGTAAAACCATTGTTTGGTAGCTCAGAACTCAGCAAGTAAATAGCAACATTTGCTGGAAGAACAGATAGTTTTTCAAATCCAATTCAAGGACTGGGTATGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCGTATCCAGGAGTTCGAGACTAGCCTGACCAACATGGTGAAACTCCGTCTCTACTAAAAATACAAAATTAGCCAGGTGTGGTGGTGGGCACCTGTAATCTCAGCTACTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGTAGGCGGAGGTTGTAGTGAGCTGAGATTGTGCCATTGCTCTCCAGCCTGGGAAACAAGAGCAAAACTCCGTCTCAAAAAAAAAAAAAATCCAATTCAAATGATTATGGAAGTAGTGGAGAAATAAACAGGAAAATGATAAATAATTAAGATAATATATAATATGGCTATATTTTAATCTATTGTTGATATGATTTTCTCTTTTCCCCTTGGGATTAGTATCTATCTCTCTACTGGATATTAATTTGTTATATTTTCTCATTAGAGCAAGTTACTCAGATGGAAAACTGAAAGCCCCTCCTAAACCATGTGCTGGCAATCAAGG', svlen=None)

Discovered due to VCF import issue - long seq had not been imported:

'AGACAGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGCACAATCTTGGCTCACTGCAAGCTCCGCCTCCCAGGTTCACACCATTCTCCTGCCTCAGCCTCCCGAGTAGCCGGGACTACAGGCGCCCACCACCACGCCCAGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTAGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCACCCACCTCGGCCTCCCAAAGCACTGGGATTACAGGCATGAGCCACCGCGCCGAGCCCCAAGACCTTTCTTTATTACCAGGGCTTCCACAGACCTGACACATGGTAGTTCCTCAATAAATAATTGCAGAATTACTGAAAAATTTTACTGTTAACTTAGGCAGTGGTAAAACCATTGTTTGGTAGCTCAGAACTCAGCAAGTAAATAGCAACATTTGCTGGAAGAACAGATAGTTTTTCAAATCCAATTCAAGGACTGGGTATGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCGTATCCAGGAGTTCGAGACTAGCCTGACCAACATGGTGAAACTCCGTCTCTACTAAAAATACAAAATTAGCCAGGTGTGGTGGTGGGCACCTGTAATCTCAGCTACTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGTAGGCGGAGGTTGTAGTGAGCTGAGATTGTGCCATTGCTCTCCAGCCTGGGAAACAAGAGCAAAACTCCGTCTCAAAAAAAAAAAAAATCCAATTCAAATGATTATGGAAGTAGTGGAGAAATAAACAGGAAAATGATAAATAATTAAGATAATATATAATATGGCTATATTTTAATCTATTGTTGATATGATTTTCTCTTTTCCCCTTGGGATTAGTATCTATCTCTCTACTGGATATTAATTTGTTATATTTTCTCATTAGAGCAAGTTACTCAGATGGAAAACTGAAAGCCCCTCCTAAACCATGTGCTGGCAATCAAGG' Traceback (most recent call last): File "/opt/variantgrid/upload/tasks/vcf/import_vcf_step_task.py", line 73, in run items_processed = self.process_items(upload_step) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/variantgrid/upload/tasks/vcf/unknown_variants_task.py", line 100, in process_items bulk_inserter.process_vcf_record(v) File "/opt/variantgrid/upload/tasks/vcf/unknown_variants_task.py", line 54, in process_vcf_record self.variant_pk_lookup.add(variant_coordinate) File "/opt/variantgrid/snpdb/variant_pk_lookup.py", line 132, in add variant_hash = self.get_variant_coordinate_hash(variant_coordinate) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/variantgrid/snpdb/variant_pk_lookup.py", line 123, in get_variant_coordinate_hash alt_id = self.sequence_pk_by_seq[variant_coordinate.alt] ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ KeyError: 'AGACAGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGCACAATCTTGGCTCACTGCAAGCTCCGCCTCCCAGGTTCACACCATTCTCCTGCCTCAGCCTCCCGAGTAGCCGGGACTACAGGCGCCCACCACCACGCCCAGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTAGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCACCCACCTCGGCCTCCCAAAGCACTGGGATTACAGGCATGAGCCACCGCGCCGAGCCCCAAGACCTTTCTTTATTACCAGGGCTTCCACAGACCTGACACATGGTAGTTCCTCAATAAATAATTGCAGAATTACTGAAAAATTTTACTGTTAACTTAGGCAGTGGTAAAACCATTGTTTGGTAGCTCAGAACTCAGCAAGTAAATAGCAACATTTGCTGGAAGAACAGATAGTTTTTCAAATCCAATTCAAGGACTGGGTATGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCGTATCCAGGAGTTCGAGACTAGCCTGACCAACATGGTGAAACTCCGTCTCTACTAAAAATACAAAATTAGCCAGGTGTGGTGGTGGGCACCTGTAATCTCAGCTACTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGTAGGCGGAGGTTGTAGTGAGCTGAGATTGTGCCATTGCTCTCCAGCCTGGGAAACAAGAGCAAAACTCCGTCTCAAAAAAAAAAAAAATCCAATTCAAATGATTATGGAAGTAGTGGAGAAATAAACAGGAAAATGATAAATAATTAAGATAATATATAATATGGCTATATTTTAATCTATTGTTGATATGATTTTCTCTTTTCCCCTTGGGATTAGTATCTATCTCTCTACTGGATATTAATTTGTTATATTTTCTCATTAGAGCAAGTTACTCAGATGGAAAACTGAAAGCCCCTCCTAAACCATGTGCTGGCAATCAAGG'

This was the VCF record:

3	37007425	1735212	A	AGACAGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGCACAATCTTGGCTCACTGCAAGCTCCGCCTCCCAGGTTCACACCATTCTCCTGCCTCAGCCTCCCGAGTAGCCGGGACTACAGGCGCCCACCACCACGCCCAGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTAGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCACCCACCTCGGCCTCCCAAAGCACTGGGATTACAGGCATGAGCCACCGCGCCGAGCCCCAAGACCTTTCTTTATTACCAGGGCTTCCACAGACCTGACACATGGTAGTTCCTCAATAAATAATTGCAGAATTACTGAAAAATTTTACTGTTAACTTAGGCAGTGGTAAAACCATTGTTTGGTAGCTCAGAACTCAGCAAGTAAATAGCAACATTTGCTGGAAGAACAGATAGTTTTTCAAATCCAATTCAAGGACTGGGTATGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCGTATCCAGGAGTTCGAGACTAGCCTGACCAACATGGTGAAACTCCGTCTCTACTAAAAATACAAAATTAGCCAGGTGTGGTGGTGGGCACCTGTAATCTCAGCTACTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGTAGGCGGAGGTTGTAGTGAGCTGAGATTGTGCCATTGCTCTCCAGCCTGGGAAACAAGAGCAAAACTCCGTCTCAAAAAAAAAAAAAATCCAATTCAAATGATTATGGAAGTAGTGGAGAAATAAACAGGAAAATGATAAATAATTAAGATAATATATAATATGGCTATATTTTAATCTATTGTTGATATGATTTTCTCTTTTCCCCTTGGGATTAGTATCTATCTCTCTACTGGATATTAATTTGTTATATTTTCTCATTAGAGCAAGTTACTCAGATGGAAAACTGAAAGCCCCTCCTAAACCATGTGCTGGCAATCAAGG	.	.	ALLELEID=1793551;CLNDISDB=MONDO:MONDO:0015356,MeSH:D009386,MedGen:C0027672,Orphanet:140162;CLNDN=Hereditary_cancer-predisposing_syndrome;CLNHGVS=NC_000003.12:g.37006055_37007053dup;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;CLNVC=Duplication;CLNVCSO=SO:1000035;GENEINFO=MLH1:4292;MC=SO:0001574|splice_acceptor_variant;ORIGIN=1

[davmlaw]

I did a quick fix and patched to VG test to be able to re-import T2T clinvar

TODO: Make a unit test for this using above example

[davmlaw]

Made unit test, and what do you know found a bug