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update e2e test files
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@apriltuesday
apriltuesday committed May 24, 2024
1 parent cde1565 commit b227f46
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Showing 8 changed files with 1,068 additions and 1,162 deletions.
7 changes: 5 additions & 2 deletions cmat/clinvar_xml_io/clinical_classification.py
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Expand Up @@ -57,8 +57,11 @@ def score(self):
@property
def clinical_significance_raw(self):
"""The original clinical significance string as stored in ClinVar. Example: 'Benign/Likely benign'."""
# TODO is this unique?
return find_mandatory_unique_element(self.class_xml, './Description').text
try:
return find_mandatory_unique_element(self.class_xml, './Description').text
except AssertionError as e:
# TODO log
return None

@property
def clinical_significance_list(self):
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34 changes: 11 additions & 23 deletions tests/pipelines/resources/expected/automated_trait_mappings.tsv
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3 changes: 0 additions & 3 deletions tests/pipelines/resources/expected/consequences_repeat.tsv
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Expand Up @@ -53,9 +53,7 @@ RCV001951015 ENSG00000160224 AIRE short_tandem_repeat_expansion
RCV001959159 ENSG00000134480 CCNH short_tandem_repeat_expansion
RCV001959159 ENSG00000145715 RASA1 short_tandem_repeat_expansion
RCV001974720 ENSG00000116127 ALMS1 short_tandem_repeat_expansion
RCV001978896 ENSG00000091483 FH short_tandem_repeat_expansion
RCV001994464 ENSG00000151914 DST short_tandem_repeat_expansion
RCV002032970 ENSG00000184634 MED12 short_tandem_repeat_expansion
RCV002072920 ENSG00000123607 TTC21B short_tandem_repeat_expansion
RCV002094328 ENSG00000148677 ANKRD1 short_tandem_repeat_expansion
RCV002113000 ENSG00000102901 CENPT short_tandem_repeat_expansion
Expand Down Expand Up @@ -124,7 +122,6 @@ RCV001051882 ENSG00000130711 PRDM12 trinucleotide_repeat_expansion
RCV001266493 ENSG00000092054 MYH7 trinucleotide_repeat_expansion
RCV001323067 ENSG00000149930 TAOK2 trinucleotide_repeat_expansion
RCV001376222 ENSG00000105618 PRPF31 trinucleotide_repeat_expansion
RCV001376222 ENSG00000237017 PRPF31-AS1 trinucleotide_repeat_expansion
RCV001410350 ENSG00000129757 CDKN1C trinucleotide_repeat_expansion
RCV001454495 ENSG00000129757 CDKN1C trinucleotide_repeat_expansion
RCV001556398 ENSG00000157764 BRAF trinucleotide_repeat_expansion
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44 changes: 0 additions & 44 deletions tests/pipelines/resources/expected/consequences_snp.tsv
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99 changes: 49 additions & 50 deletions tests/pipelines/resources/expected/consequences_structural.tsv
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Original file line number Diff line number Diff line change
@@ -1,10 +1,22 @@
NC_000013.11:g.93997007_94063501del66495insATAAATCACTTAGAGATGT ENSG00000183098 GPC6 feature_truncation
NC_000013.11:g.94252984_94352299del99316insCTA ENSG00000183098 GPC6 feature_truncation
NC_000014.9:g.91881408_91904133dup ENSG00000140092 FBLN5 feature_elongation
NC_000012.12:g.109581396_109581551del ENSG00000110921 MVK stop_lost
NC_000001.11:g.1696548_1732685del ENSG00000008128 CDK11A transcript_ablation
NC_000001.11:g.49462391_49524663del ENSG00000186094 AGBL4 intron_variant
NC_000003.12:g.89335416_89368021del ENSG00000044524 EPHA3 feature_truncation
NC_000017.11:g.79369452_79395919dup ENSG00000167281 RBFOX3 intron_variant
NC_000002.12:g.32113664_32125322del ENSG00000021574 SPAST feature_truncation
NC_000021.9:g.21045800_21077901del ENSG00000154654 NCAM2 intron_variant
NC_000008.11:g.19411890_19467180del ENSG00000147408 CSGALNACT1 feature_truncation
NC_000001.11:g.216263262_216311879del ENSG00000042781 USH2A feature_truncation
NC_000023.11:g.32622009_32644156del ENSG00000198947 DMD feature_truncation
NC_000023.11:g.32622009_32644156del ENSG00000221348 MIR548F5 transcript_ablation
NC_000001.11:g.215999483_216183366del ENSG00000042781 USH2A stop_lost
NC_000002.12:g.47439264_47450433del ENSG00000095002 MSH2 stop_lost
NC_000004.12:g.68626601_68646936del ENSG00000196620 UGT2B15 feature_truncation
NC_000003.12:g.113857357_113901499del ENSG00000178075 GRAMD1C feature_truncation
NC_000011.10:g.5433500_5475233dup ENSG00000167359 OR51I1 transcript_amplification
NC_000011.10:g.5433500_5475233dup ENSG00000187918 OR51I2 transcript_amplification
NC_000011.10:g.5433500_5475233dup ENSG00000196565 HBG2 intron_variant
NC_000011.10:g.5433500_5475233dup ENSG00000213931 HBE1 intron_variant
NC_000001.11:g.1696548_1732685del ENSG00000008128 CDK11A transcript_ablation
NC_000007.14:g.152176768_152580446dup ENSG00000055609 KMT2C transcript_amplification
NC_000017.11:g.3602749_3678945del ENSG00000040531 CTNS transcript_ablation
NC_000017.11:g.3602749_3678945del ENSG00000083454 P2RX5 stop_lost
Expand All @@ -16,7 +28,9 @@ NC_000017.11:g.46092442_46502770dup ENSG00000120071 KANSL1 transcript_amplificat
NC_000017.11:g.46092442_46502770dup ENSG00000176681 LRRC37A transcript_amplification
NC_000017.11:g.46092442_46502770dup ENSG00000185829 ARL17A 3_prime_UTR_variant
NC_000017.11:g.46092442_46502770dup ENSG00000228696 ARL17B transcript_amplification
NC_000017.11:g.79369452_79395919dup ENSG00000167281 RBFOX3 intron_variant
NC_000023.11:g.154015897_154030807del ENSG00000169057 MECP2 stop_lost
NC_000023.11:g.154015897_154030807del ENSG00000184216 IRAK1 feature_truncation
NC_000023.11:g.154015897_154030807del ENSG00000284286 MIR718 transcript_ablation
NC_000014.9:g.95696766_96390792dup ENSG00000066739 ATG2B transcript_amplification
NC_000014.9:g.95696766_96390792dup ENSG00000100721 TCL1A transcript_amplification
NC_000014.9:g.95696766_96390792dup ENSG00000100739 BDKRB1 transcript_amplification
Expand All @@ -26,7 +40,33 @@ NC_000014.9:g.95696766_96390792dup ENSG00000227051 C14orf132 transcript_amplific
NC_000014.9:g.95696766_96390792dup ENSG00000250366 TUNAR transcript_amplification
NC_000002.12:g.32147746_32173488del ENSG00000021574 SPAST stop_lost
NC_000002.12:g.32147746_32173488del ENSG00000152683 SLC30A6 feature_truncation
NC_000002.12:g.32113664_32125322del ENSG00000021574 SPAST feature_truncation
NC_000012.12:g.23484745_23564581del ENSG00000134532 SOX5 stop_lost
NC_000014.9:g.78581479_79053758del ENSG00000021645 NRXN3 transcript_ablation
NC_000006.12:g.5609990_5726136del ENSG00000145982 FARS2 feature_truncation
NC_000001.11:g.45650769_45929717dup ENSG00000086015 MAST2 coding_sequence_variant
NC_000001.11:g.45650769_45929717dup ENSG00000159592 GPBP1L1 coding_sequence_variant
NC_000001.11:g.45650769_45929717dup ENSG00000159596 TMEM69 transcript_amplification
NC_000001.11:g.45650769_45929717dup ENSG00000197429 IPP transcript_amplification
NC_000006.12:g.259881_303298dup ENSG00000112679 DUSP22 coding_sequence_variant
NC_000010.11:g.133438823_133565257del ENSG00000130649 CYP2E1 transcript_ablation
NC_000010.11:g.133438823_133565257del ENSG00000171772 SYCE1 stop_lost
NC_000010.11:g.133438823_133565257del ENSG00000214279 SCART1 transcript_ablation
NC_000007.14:g.1687729_1779914del ENSG00000225968 ELFN1 stop_lost
NC_000014.9:g.87925163_87956828del ENSG00000054983 GALC stop_lost
NC_000015.10:g.51681311_51791472dup ENSG00000104112 SCG3 transcript_amplification
NC_000015.10:g.51681311_51791472dup ENSG00000128872 TMOD2 coding_sequence_variant
NC_000015.10:g.51681311_51791472dup ENSG00000140280 LYSMD2 transcript_amplification
NC_000007.14:g.152052676_152295696del ENSG00000055609 KMT2C transcript_ablation
NC_000007.14:g.152052676_152295696del ENSG00000178234 GALNT11 transcript_ablation
NC_000015.10:g.22723843_23122692dup ENSG00000140157 NIPA2 transcript_amplification
NC_000015.10:g.22723843_23122692dup ENSG00000170113 NIPA1 transcript_amplification
NC_000015.10:g.22723843_23122692dup ENSG00000273749 CYFIP1 transcript_amplification
NC_000015.10:g.22723843_23122692dup ENSG00000275835 TUBGCP5 transcript_amplification
NC_000023.11:g.136487348_136507517dup ENSG00000102239 BRS3 transcript_amplification
NC_000023.11:g.136487348_136507517dup ENSG00000102241 HTATSF1 transcript_amplification
NC_000023.11:g.41506506_41542250del ENSG00000147044 CASK transcript_ablation
NC_000002.12:g.196873396_196873397insTTCT ENSG00000197121 PGAP1 intron_variant
NC_000015.10:g.48428344_48428355del ENSG00000166147 FBN1 feature_truncation
NC_000001.11:g.196608263_197002575del ENSG00000000971 CFH transcript_ablation
NC_000001.11:g.196608263_197002575del ENSG00000080910 CFHR2 transcript_ablation
NC_000001.11:g.196608263_197002575del ENSG00000116785 CFHR3 transcript_ablation
Expand Down Expand Up @@ -60,49 +100,8 @@ NC_000017.11:g.9701182_11983353del ENSG00000214978 GSG1L2 transcript_ablation
NC_000017.11:g.9701182_11983353del ENSG00000233670 PIRT transcript_ablation
NC_000017.11:g.9701182_11983353del ENSG00000263429 TMEM238L transcript_ablation
NC_000017.11:g.9701182_11983353del ENSG00000264424 MYH4 transcript_ablation
NC_000012.12:g.23484745_23564581del ENSG00000134532 SOX5 stop_lost
NC_000004.12:g.68626601_68646936del ENSG00000196620 UGT2B15 feature_truncation
NC_000003.12:g.113857357_113901499del ENSG00000178075 GRAMD1C feature_truncation
NC_000014.9:g.78581479_79053758del ENSG00000021645 NRXN3 transcript_ablation
NC_000017.11:g.43081201_43091610del ENSG00000012048 BRCA1 feature_truncation
NC_000002.12:g.47439264_47450433del ENSG00000095002 MSH2 stop_lost
NC_000016.10:g.16151250_16167657del ENSG00000091262 ABCC6 feature_truncation
NC_000006.12:g.5609990_5726136del ENSG00000145982 FARS2 feature_truncation
NC_000001.11:g.216263262_216311879del ENSG00000042781 USH2A feature_truncation
NC_000001.11:g.215999483_216183366del ENSG00000042781 USH2A stop_lost
NC_000001.11:g.45650769_45929717dup ENSG00000086015 MAST2 coding_sequence_variant
NC_000001.11:g.45650769_45929717dup ENSG00000159592 GPBP1L1 coding_sequence_variant
NC_000001.11:g.45650769_45929717dup ENSG00000159596 TMEM69 transcript_amplification
NC_000001.11:g.45650769_45929717dup ENSG00000197429 IPP transcript_amplification
NC_000006.12:g.259881_303298dup ENSG00000112679 DUSP22 coding_sequence_variant
NC_000010.11:g.133438823_133565257del ENSG00000130649 CYP2E1 transcript_ablation
NC_000010.11:g.133438823_133565257del ENSG00000171772 SYCE1 stop_lost
NC_000010.11:g.133438823_133565257del ENSG00000214279 SCART1 transcript_ablation
NC_000011.10:g.5433500_5475233dup ENSG00000167359 OR51I1 transcript_amplification
NC_000011.10:g.5433500_5475233dup ENSG00000187918 OR51I2 transcript_amplification
NC_000011.10:g.5433500_5475233dup ENSG00000196565 HBG2 intron_variant
NC_000011.10:g.5433500_5475233dup ENSG00000213931 HBE1 intron_variant
NC_000021.9:g.21045800_21077901del ENSG00000154654 NCAM2 intron_variant
NC_000023.11:g.41506506_41542250del ENSG00000147044 CASK transcript_ablation
NC_000008.11:g.19411890_19467180del ENSG00000147408 CSGALNACT1 feature_truncation
NC_000007.14:g.1687729_1779914del ENSG00000225968 ELFN1 stop_lost
NC_000014.9:g.87925163_87956828del ENSG00000054983 GALC stop_lost
NC_000002.12:g.196873396_196873397insTTCT ENSG00000197121 PGAP1 intron_variant
NC_000015.10:g.51681311_51791472dup ENSG00000104112 SCG3 transcript_amplification
NC_000015.10:g.51681311_51791472dup ENSG00000128872 TMOD2 coding_sequence_variant
NC_000015.10:g.51681311_51791472dup ENSG00000140280 LYSMD2 transcript_amplification
NC_000007.14:g.152052676_152295696del ENSG00000055609 KMT2C transcript_ablation
NC_000007.14:g.152052676_152295696del ENSG00000178234 GALNT11 transcript_ablation
NC_000023.11:g.136487348_136507517dup ENSG00000102239 BRS3 transcript_amplification
NC_000023.11:g.136487348_136507517dup ENSG00000102241 HTATSF1 transcript_amplification
NC_000015.10:g.22723843_23122692dup ENSG00000140157 NIPA2 transcript_amplification
NC_000015.10:g.22723843_23122692dup ENSG00000170113 NIPA1 transcript_amplification
NC_000015.10:g.22723843_23122692dup ENSG00000273749 CYFIP1 transcript_amplification
NC_000015.10:g.22723843_23122692dup ENSG00000275835 TUBGCP5 transcript_amplification
NC_000023.11:g.154015897_154030807del ENSG00000169057 MECP2 stop_lost
NC_000023.11:g.154015897_154030807del ENSG00000184216 IRAK1 feature_truncation
NC_000023.11:g.154015897_154030807del ENSG00000284286 MIR718 transcript_ablation
NC_000002.12:g.202377525_202519014del141490 ENSG00000204217 BMPR2 feature_truncation
NC_000015.10:g.48428344_48428355del ENSG00000166147 FBN1 feature_truncation
NC_000023.11:g.32622009_32644156del ENSG00000198947 DMD feature_truncation
NC_000023.11:g.32622009_32644156del ENSG00000221348 MIR548F5 transcript_ablation
NC_000017.11:g.43081201_43091610del ENSG00000012048 BRCA1 feature_truncation
NC_000013.11:g.93997007_94063501del66495insATAAATCACTTAGAGATGT ENSG00000183098 GPC6 feature_truncation
NC_000013.11:g.94252984_94352299del99316insCTA ENSG00000183098 GPC6 feature_truncation
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