Feature/31243/leeds crc refactor #76
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,187 @@ | ||
| module Import | ||
| module Helpers | ||
| module Colorectal | ||
| module Providers | ||
| module Rr8 | ||
| # Constants used by Leeds Colorectal | ||
| module Constants | ||
| TEST_SCOPE_MAP_COLO = { 'carrier test' => :targeted_mutation, | ||
| 'confirmation' => :targeted_mutation, | ||
| 'diagnostic' => :full_screen, | ||
| 'diagnostic; fap' => :full_screen, | ||
| 'diagnostic; lynch' => :full_screen, | ||
| 'diagnostic; pms2' => :full_screen, | ||
| 'predictive' => :targeted_mutation, | ||
| 'predictive test' => :targeted_mutation, | ||
| 'r209.1' => :full_screen, | ||
| 'r209.2' => :full_screen, | ||
| 'r210.5' => :full_screen, | ||
| 'r210.2' => :full_screen, | ||
| 'r211.1' => :full_screen, | ||
| 'r211.2' => :full_screen, | ||
| 'familial' => :targeted_mutation }.freeze | ||
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| TEST_TYPE_MAP_COLO = { 'carrier test' => :carrier, | ||
| 'diagnostic' => :diagnostic, | ||
| 'diagnostic; fap' => :diagnostic, | ||
| 'diagnostic; lynch' => :diagnostic, | ||
| 'confirmation' => :diagnostic, | ||
| 'predictive' => :predictive, | ||
| 'predictive test' => :predictive, | ||
| 'familial' => :predictive }.freeze | ||
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| PASS_THROUGH_FIELDS = %w[age consultantcode | ||
| providercode | ||
| receiveddate | ||
| authoriseddate | ||
| requesteddate | ||
| servicereportidentifier | ||
| organisationcode_testresult | ||
| specimentype].freeze | ||
| FIELD_NAME_MAPPINGS = { 'consultantcode' => 'practitionercode', | ||
| 'instigated_date' => 'requesteddate' }.freeze | ||
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| GENES = 'APC|ATM|BAP1|BMPR1A|BRCA1|BRCA2|CHEK2|EPCAM|FH|FLCN|GREM1|MET| | ||
| MLH1|MSH2|MSH6|MUTYH|NTHL1|PALB2|PMS2|POLD1|POLE|PTEN|RAD51C|RAD51D| | ||
| RNF43|SDHB|SMAD4|STK11|TP53|VHL'.freeze | ||
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| # rubocop:disable Lint/MixedRegexpCaptureTypes | ||
| MMR_GENE_REGEX = /APC|BMPR1A|EPCAM|GREM1|MLH1|MSH2|MSH6|MUTYH|NTHL1|PMS2|POLD1| | ||
| POLE|PTEN|SMAD4|STK11/ix | ||
| CDNA_REGEX = /c\.(?<cdna>[\w+>*\-]+)?/ix | ||
| PROTEIN_REGEX = /\(?p\.\(?(?<impact>\w+)\)?/ix | ||
| EXON_REGEX = /(?<exon>exon(s)?[\s\-\d]+)/ix | ||
| GENE_FAIL_REGEX = /(?=(?<gene>#{GENES})[\w\s]+fail)/ix | ||
| NOPATH_REGEX = /.No pathogenic variant was identified./i | ||
| EXON_VARIANT_REGEX = /(?<variant>del|dup|ins).+ex(on)?s?\s? | ||
| (?<exons>[0-9]+(-[0-9]+)?)| | ||
| ex(on)?s?\s?(?<exons>[0-9]+(-[0-9]+)?)\s? | ||
| (?<variant>del|dup|ins)| | ||
| ex(on)?s?\s?(?<exons>[0-9]+\s?(\s?-\s?[0-9]+)?)\s? | ||
| (?<variant>del|dup|ins)?| | ||
|
There was a problem hiding this comment. Are lines 60-61 similar to 58-59 but with a few extra optional values- could this be simplified? |
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| (?<variant>del|dup|ins)\s?(?<exons>[0-9]+(?<dgs>-[0-9]+)?)| | ||
| ex(on)?s?\s?(?<exons>[0-9]+(\sto\s[0-9]+)?)\s | ||
| (?<variant>del|dup|ins)| | ||
| x(?<exons>[0-9+-? ]+)+(?<variant>del|dup|ins)| | ||
| ex(on)?s?[\s\w,]+(?<variant>del|dup|ins)| | ||
| (?<variant>del|dup|ins)[\s\w]+gene/ix | ||
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| COLORECTAL_GENES_REGEX = /(?<colorectal>#{GENES})/x | ||
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| VARIANT_REPORT_REGEX = /(?<report>(hetero|homo)zygo[\w\s\-.>():=,'+]+)+/ix | ||
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| EXONIC_REPORT_REGEX = /(?<report>(#{GENES})\sexon(s)?[\w\s\-.>():=,&]+)/ix | ||
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| PATHOGENIC_REPORT_REGEX = /(?<report>pathogenic\s(#{GENES})[\w\s\-.>():=,&]+)/ix | ||
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There was a problem hiding this comment. If you have "." as one of the options in the square brackets, do you need the rest of the options if "." includes all of the other characters you have listed? |
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| TARG_GENE_REGEX = /(?<report>(#{GENES})[\w\s]+(c\.[\w\s\-.>():=,']+))/ix | ||
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| ABSENT_REGEX = /is absent in this patient/i | ||
| NO_DEL_REGEX = /this patient does not have the deletion/i | ||
| PATHOGENIC_REGEX = /(?<pathogenic>likely\snon-pathogenic|likely\spathogenic| | ||
| likely\s(to\sbe\s)?pathogenic|pathogenic[^ity]|benign|likely\s(to\sbe\s)?benign| | ||
| uncertain\s(clinical\s)?significance)/ix | ||
| PATHOGENIC_GENES_REGEX = /(?<pathogenic>likely\snon-pathogenic|likely\spathogenic| | ||
| pathogenic[^ity]|benign|likely\s(to\sbe\s)?benign| | ||
| uncertain\s(clinical\s)?significance)[\w\s\W]*(?<assocgene>#{GENES})/ix | ||
| GENE_PATH_REGEX = /(?<assocgene>#{GENES})[\w\s\W]*(?<pathogenic>likely\snon-pathogenic| | ||
| likely\spathogenic|pathogenic[^ity]|benign|likely\s(to\sbe\s)?benign| | ||
| uncertain\s(clinical\s)?significance)/ix | ||
| # rubocop:enable Lint/MixedRegexpCaptureTypes | ||
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| GENES_FILEPATH = 'lib/import/helpers/colorectal/providers/rr8/genes.yml'.freeze | ||
| STATUS_FILEPATH = 'lib/import/helpers/colorectal/providers/rr8/status.yml'.freeze | ||
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| GENES_PANEL = { | ||
| 'apc' => %w[APC], | ||
| 'epcam' => %w[EPCAM], | ||
| 'mlh1' => %w[MLH1], | ||
| 'mlh1_msh2' => %w[MLH1 MSH2], | ||
| 'mlh1_msh2_msh6' => %w[MLH1 MSH2 MSH6], | ||
| 'mlh1_pms2' => %w[MLH1 PMS2], | ||
| 'pms2_mutyh' => %w[MUTYH PMS2], | ||
| 'msh2' => %w[MSH2], | ||
| 'msh6' => %w[MSH6], | ||
| 'mutyh' => %w[MUTYH], | ||
| 'pms2' => %w[PMS2] | ||
| }.freeze | ||
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| STATUS_PANEL = { | ||
| 'unknown' => 4, | ||
| 'normal' => 1, | ||
| 'abnormal' => 2, | ||
| 'normal_var' => 10, | ||
| 'fail' => 9 | ||
| }.freeze | ||
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| VARIANT_CLASS_5 = [ | ||
| 'conf mlpa +ve', | ||
| 'mlh1 confirmation +ve', | ||
| 'mlpa del confirmation +ve', | ||
| 'msh2 confirmation +ve', | ||
| 'mlpa +ve(large exon deletion) + seq -ve', | ||
| 'mlpa multi-exon deletion (with seq)', | ||
| 'ngs class m', | ||
| 'sequencing positive', | ||
| 'pred mlpa epcam del +ve', | ||
| 'pred mlpa msh2 del +ve', | ||
| 'pred mlpa msh2 dup +ve', | ||
| 'pred mlpa msh6 del +ve', | ||
| 'pred seq mlh1 +ve', | ||
| 'pred seq msh2 +ve', | ||
| 'pred seq msh6 +ve', | ||
| 'confirmation_seq_positive', | ||
| 'diagnostic apc +ve', | ||
| 'predictive_seq_positive', | ||
| 'seq mutation +ve', | ||
| 'biallelic pred positive', | ||
| 'mlpa pred positive', | ||
| 'pred complex mut +ve', | ||
| 'r802x homozygote (diag)', | ||
| 'seq pred positive', | ||
| 'apc - conf mlpa +ve', | ||
| 'fap diagn mutyh het.', | ||
| 'conf seq +ve (apc)', | ||
| 'conf seq +ve (mutyh)', | ||
| 'fap conf-pred +ve (apc)', | ||
| 'fap diagn +ve (apc)', | ||
| 'fap diagn +ve (mutyh c.het)', | ||
| 'fap diagn +ve (mutyh homoz)', | ||
| 'fap diagn mutyh het.', | ||
| '(v2) mutyh het.', | ||
| 'apc - conf seq +ve' | ||
| ].freeze | ||
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| VARIANT_CLASS_7 = [ | ||
| 'conf seq +ve', | ||
| 'mlpa -ve + seq (splice site mutation)', | ||
| 'mlpa -ve + seq +ve (nonsense/frameshift)', | ||
| 'ngs mlh1 truncating/frameshift', | ||
| 'ngs msh2 truncating/frameshift', | ||
| 'ngs multiple exon mlpa del', | ||
| 'pred mlpa +ve', | ||
| 'mlpa positive', | ||
| 'mlpa positive (diag)', | ||
| 'pred (other) positive', | ||
| 'generic c4/5', | ||
| 'lynch diag; c4/5', | ||
| 'generic c4/5', | ||
| 'lynch diag; c4/5', | ||
| 'r210_c4/5', | ||
| 'lynch diag; c4/5', | ||
| 'generic c4/5' | ||
| ].freeze | ||
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| NON_PATH_VARCLASS = [ | ||
| 'likely benign', | ||
| 'likely to be benign', | ||
| 'non-pathological variant', | ||
| 'likely non-pathogenic', | ||
| 'benign' | ||
| ].freeze | ||
| end | ||
| end | ||
| end | ||
| end | ||
| end | ||
| end | ||
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As this is an update to the assigning variant class in the genotype.rb file, have you checked that it won't affect any of the other importers?
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Its extending the range that's allowed to be in variantpathclass and adheres to Zvariantpathclass. If any other importer is able to extract c4/5 pathogenicity values and map upto 7 in future that should be fine.