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Feature/rmh brca #67

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merged 15 commits into from
Feb 28, 2024
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Merged

Feature/rmh brca #67

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dcb7c09
Add Royal Marsden changes for test status=10
lauramccluskey1 Aug 31, 2023
de9fcdc
add unittests for royal marsden test status=10
lauramccluskey1 Aug 31, 2023
4167579
update non pathogenic variant changes
lauramccluskey1 Sep 4, 2023
5103d9b
update unittests for non pathogenic variant changes to royal marsden
lauramccluskey1 Sep 4, 2023
d00452f
make rubocop changes
lauramccluskey1 Sep 4, 2023
b84e69b
Merge develop branch into feature/RMH_brca
lauramccluskey1 Sep 4, 2023
80c9d2d
fix nil error
lauramccluskey1 Sep 5, 2023
6dc4265
Merge branch 'develop' into feature/RMH_brca
lauramccluskey1 Nov 10, 2023
6e70dc3
move process_teststatus after process_variant to prevent teststatus b…
lauramccluskey1 Nov 16, 2023
424346b
merge develop into branch feature/RMH_brca
lauramccluskey1 Jan 8, 2024
b0c614c
Merge branch 'develop' into feature/RMH_brca
lauramccluskey1 Feb 2, 2024
6e4bd38
Merge branch 'develop' into feature/RMH_brca
lauramccluskey1 Feb 16, 2024
1c81ce7
changes from code review and rubocop
lauramccluskey1 Feb 21, 2024
6e86452
merge develop into feature/RMH_brca
lauramccluskey1 Feb 28, 2024
a7f7fa0
correct spelling error
lauramccluskey1 Feb 28, 2024
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46 changes: 35 additions & 11 deletions lib/import/brca/providers/royal_marsden/royal_marsden_handler.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -22,12 +22,15 @@ class RoyalMarsdenHandler < Import::Germline::ProviderHandler
'2b' => 2,
'2c' => 3,
'variant' => 2 }.freeze
NON_PATH_VARIANT_CLASS = { '2a' => 1,
'2b' => 2,
'variant' => 2 }.freeze

TEST_TYPE_MAP = { 'affected' => :diagnostic,
'unaffected' => :predictive }.freeze
# rubocop:disable Lint/MixedRegexpCaptureTypes
CDNA_REGEX_PROT = /c\.(?<cdna>.+)(?=(?<separtors>_|;.)p\.(?<impact>.+))/i.freeze
CDNA_REGEX_NOPROT = /c\.(?<cdna>.+)/i.freeze
CDNA_REGEX_PROT = /c\.(?<cdna>.+)(?=(?<separators>_|;.)p\.(?<impact>.+))/i
CDNA_REGEX_NOPROT = /c\.(?<cdna>.+)/i
DEL_DUP_REGEX = /(?<deldup>Deletion|Duplication)\s(ex|exon)s?\s?
(?<exon>\d+([a-z -]+\d+)?)|
(exon|ex)s?\s?(?<exon>\d+([a-z -]+\d+)?)\s?
Expand All @@ -50,8 +53,8 @@ def process_fields(record)
record.raw_fields,
PASS_THROUGH_FIELDS)
process_varpathclass(genotype, record)
process_teststatus(genotype, record)
process_variant(genotype, record)
process_teststatus(genotype, record)
process_large_deldup(genotype, record)
process_test_scope(genotype, record)
process_test_type(genotype, record)
Expand Down Expand Up @@ -85,6 +88,7 @@ def process_varpathclass(genotype, record)
@logger.debug 'NO VARIANT PATHCLASS DETECTED'
return
end

varpathclass = record.raw_fields['variantpathclass'].downcase.strip
# unless record.raw_fields['variantpathclass'].nil?
# if varpathclass.present? && VARIANT_PATH_CLASS[varpathclass]
Expand All @@ -98,15 +102,24 @@ def process_teststatus(genotype, record)
@logger.debug 'UNABLE TO DETERMINE TESTSTATUS'
return
end

teststatus = record.raw_fields['teststatus']
nonpathvarclass = record.raw_fields['variantpathclass']&.downcase&.strip
# unless record.raw_fields['teststatus'].nil?
if normal_test?(teststatus)
genotype.add_status(1)
elsif failed_test?(teststatus)
process_assign_teststatus(genotype, teststatus, nonpathvarclass)
end

def process_assign_teststatus(genotype, teststatus, nonpathvarclass)
if failed_test?(teststatus)
genotype.add_status(9)
genotype.add_variant_class(nil)
elsif non_pathogenic_variant_test?(teststatus, nonpathvarclass)
genotype.add_status(10)
elsif positive_test?(teststatus)
genotype.add_status(2)
elsif normal_test?(teststatus)
genotype.add_status(1)
elsif borderline_test?(teststatus)
genotype.add_status(7)
end
end

Expand Down Expand Up @@ -154,7 +167,6 @@ def process_large_deldup(genotype, record)

def normal_test?(teststatus)
%r{NO PATHOGENIC (VARIANT|DEL/DUP) IDENTIFIED}.match(teststatus) ||
/non-pathogenic variant detected/.match(teststatus) ||
/No mutation detected/.match(teststatus)
end

Expand All @@ -164,9 +176,21 @@ def failed_test?(teststatus)

def positive_test?(teststatus)
/c\..+/.match(teststatus) ||
/Deletion*/.match(teststatus) ||
/Duplication*/.match(teststatus) ||
/Exon*/i.match(teststatus)
/Deletion.*/.match(teststatus) ||
/Duplication.*/.match(teststatus) ||
/Exon.*/i.match(teststatus) ||
/Del.*ex\s?1*/i.match(teststatus) ||
/Ex.*del/i.match(teststatus) ||
/BRCA.*exon.*Deletion/i.match(teststatus)
end

def borderline_test?(teststatus)
/borderline/.match(teststatus)
end

def non_pathogenic_variant_test?(teststatus, nonpathvarclass)
/non-pathogenic\svariant\sdetected/i.match(teststatus) ||
NON_PATH_VARIANT_CLASS[nonpathvarclass]
end
end
end
Expand Down
48 changes: 48 additions & 0 deletions test/lib/import/brca/providers/royal_marsden/royal_marsden_handler_test.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,54 @@ def setup
normal_record.raw_fields['teststatus'] = 'NO PATHOGENIC VARIANT IDENTIFIED'
@handler.process_teststatus(@genotype, normal_record)
assert_equal 1, @genotype.attribute_map['teststatus']

non_path_record = build_raw_record('pseudo_id1' => 'bob')
non_path_record.raw_fields['teststatus'] = 'Ex del'
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Can raw_fields be passed to the build_raw_record method, eg:

broken_record = build_raw_record('pseudo_id1' => 'bob', raw_fields: { 'teststatus' => 'Ex del' } )

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Thanks for the suggestion @ollietulloch ! I have tried that and it doesn't work- I think its because build new record adds the test status field by loading the rawtext_clinical_json. So that needs to be loaded first then we can update the test status afterwards. Let me know if there is another way!

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Ah ok, perhaps something for a future PR. It'd be nice for build_raw_record to be able to popluate raw_fields

non_path_record.raw_fields['variantpathclass'] = '2a'
@handler.process_teststatus(@genotype, non_path_record)
assert_equal 10, @genotype.attribute_map['teststatus']

non_path_record = build_raw_record('pseudo_id1' => 'bob')
non_path_record.raw_fields['teststatus'] = 'Ex del'
non_path_record.raw_fields['variantpathclass'] = '2b'
@handler.process_teststatus(@genotype, non_path_record)
assert_equal 10, @genotype.attribute_map['teststatus']

non_path_record = build_raw_record('pseudo_id1' => 'bob')
non_path_record.raw_fields['teststatus'] = 'Ex del'
non_path_record.raw_fields['variantpathclass'] = 'variant'
@handler.process_teststatus(@genotype, non_path_record)
assert_equal 10, @genotype.attribute_map['teststatus']

path_record = build_raw_record('pseudo_id1' => 'bob')
path_record.raw_fields['teststatus'] = 'Ex Del'
path_record.raw_fields['variantpathclass'] = '1b'
@handler.process_teststatus(@genotype, path_record)
assert_equal 2, @genotype.attribute_map['teststatus']

path_record = build_raw_record('pseudo_id1' => 'bob')
path_record.raw_fields['teststatus'] = 'Del ex 1'
path_record.raw_fields['variantpathclass'] = '1b'
@handler.process_teststatus(@genotype, path_record)
assert_equal 2, @genotype.attribute_map['teststatus']

path_record = build_raw_record('pseudo_id1' => 'bob')
path_record.raw_fields['teststatus'] = 'BRCA exon Deletion'
path_record.raw_fields['variantpathclass'] = '1b'
@handler.process_teststatus(@genotype, path_record)
assert_equal 2, @genotype.attribute_map['teststatus']

path_record = build_raw_record('pseudo_id1' => 'bob')
path_record.raw_fields['teststatus'] = 'borderline'
path_record.raw_fields['variantpathclass'] = '1b'
@handler.process_teststatus(@genotype, path_record)
assert_equal 7, @genotype.attribute_map['teststatus']

path_record = build_raw_record('pseudo_id1' => 'bob')
path_record.raw_fields['teststatus'] = 'non-pathogenic variant detected'
path_record.raw_fields['variantpathclass'] = '1b'
@handler.process_teststatus(@genotype, path_record)
assert_equal 10, @genotype.attribute_map['teststatus']
end

test 'process_variant' do
Expand Down
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