def test_blankRowsFilter_When_buildFinalTemplateIsCalled_Return_blankList(
self):
blankrow1 = []
blankrow2 = []
tsvInputRow = {
'alt_allele': '-',
'read_depth': '11572',
'ensembl_gene_id': '',
'rs_id_Variant': '',
'Platform': 'Targeted NGS',
'ucsc_gene_id': '',
'ref_allele': 'T',
'chromosome': '19',
'ncbi_gene_id': '',
'nucleotide_change': '1225delA',
'hgnc_symbol': 'KEAP1',
'consequence': 'stop gain',
'Allele_frequency': '96,47',
'Passage': '27',
'amino_acid_change': 'M409X',
'Model_ID': 'LCF16',
'datasource': 'CURIE-LC',
'ensembl_transcript_id': '',
'Sample_ID': 'LCF16p27:26/08/2016',
'seq_start_position': '10491677',
'genome_assembly': 'GRCh38',
'sample_origin': 'xenograft'
}
inputRows = ps.DataFrame([blankrow1, blankrow2])
actualRow = AnnotationMerger.buildFinalTemplate(inputRows, tsvInputRow)
self.assertEquals(len(actualRow), 0)
def test_GivenTwoEmblRow_When_buildFinalTemplateIsCalled_Return_BuiltRowWithoutNCBIdata(
self):
emblGene = "ENSG00000068078"
emblFeature = "ENST00000260795"
emblGene2 = "ENSG0000000999"
emblFeature2 = 'ENST000000111'
emblRow = [
"4_1804915_A/G", "4:1804915", "G", emblGene, emblFeature,
"Transcript", "3_prime_UTR_variant", "1509", "-", "-", "-", "-",
"rs1466726466",
"IMPACT=MODIFIER;STRAND=1;VARIANT_CLASS=SNV;SYMBOL=FGFR3;SYMBOL_SOURCE=HGNC;HGNC_ID=HGNC "
]
emblRow2 = [
"4_1804915_A/G", "4:1804916", "G", emblGene2, emblFeature2,
"Transcript", "missense", "1509", "-", "-", "-", "-",
"rs1466726466",
"IMPACT=High;STRAND=1;VARIANT_CLASS=SNV;SYMBOL=FGFR3;SYMBOL_SOURCE=HGNC;HGNC_ID=HGNC "
]
colNames = [
"#Uploaded_variation", "Location", "Allele", "Gene", "Feature",
"Feature_type", "Consequence", "cDNA_position", "CDS_position",
"Protein_position", "Amino_acids", "Codons", "Existing_variation",
"Extra"
]
tsvInputRow = {
'alt_allele': '-',
'read_depth': '11572',
'ensembl_gene_id': '',
'rs_id_Variant': '',
'Platform': 'Targeted NGS',
'ucsc_gene_id': '',
'ref_allele': 'T',
'chromosome': '19',
'ncbi_gene_id': '',
'nucleotide_change': '1225delA',
'hgnc_symbol': 'KEAP1',
'consequence': 'stop gain',
'Allele_frequency': '96,47',
'Passage': '27',
'amino_acid_change': 'M409X',
'Model_ID': 'LCF16',
'datasource': 'CURIE-LC',
'ensembl_transcript_id': '',
'Sample_ID': 'LCF16p27:26/08/2016',
'seq_start_position': '10491677',
'genome_assembly': 'GRCh38',
'sample_origin': 'xenograft'
}
inputRows = ps.DataFrame([emblRow, emblRow2], columns=colNames)
actualRow = AnnotationMerger.buildFinalTemplate(inputRows, tsvInputRow)
self.assertEquals(actualRow[20], None)
self.assertEquals(actualRow[21], None)
self.assertEquals(actualRow[22], emblGene)
self.assertEquals(actualRow[23], emblFeature)
def test_buildFinalAnnotation_realDroppedAnnotations_Debug(self):
AnnotationMerger.buildFinalTemplate()
def test_GivenTwoMatchingColumns_WhenRowBuilderIsCalled_Then_ReturnCorrectlyBuiltRow(
self):
emblGene = "ENSG00000068078"
emblFeature = "ENST00000260795"
ncbiGene = "9817"
ncbiFeature = 'NM_203500.2'
emblRow = ["4_1804915_A/G", "4:1804915", "G", emblGene, emblFeature, "Transcript",
"3_prime_UTR_variant", \
"1509", "-", "-", "-", "-", "rs1466726466", \
"IMPACT=MODIFIER;STRAND=1;VARIANT_CLASS=SNV;SYMBOL=FGFR3;SYMBOL_SOURCE=HGNC;HGNC_ID=HGNC "]
ncbiRow = {
'Feature_type': 'Transcript',
'Extra': 'IMPACT=HIGH;STRAND=-1;VARIANT_'
'CLASS=deletion;SYMBOL=KEAP1;SYMBOL_SOURCE=EntrezGene;HGNC_ID=HGNC:23177;BIOTYPE=protein_coding;CANONICAL=YES;ENSP=NP_987096.1;SOURCE=RefSeq;GIVEN_REF=T;USED_REF=T;EXON=3/6;HGVSc=NM_203500.2:c.1225del;HGVSp=NP_987096.1:p.Met409Ter',
'#Uploaded_variation': '19_10491677_T/-',
'cDNA_position': '1388',
'Feature': ncbiFeature,
'Codons': 'Atg/tg',
'Existing_variation': '-',
'Location': '19:10491677',
'CDS_position': '1225',
'Protein_position': '409',
'Consequence': 'frameshift_variant',
'Allele': '-',
'Gene': ncbiGene,
'Amino_acids': 'M/X'
}
colNames = [
"#Uploaded_variation", "Location", "Allele", "Gene", "Feature",
"Feature_type", "Consequence", "cDNA_position", "CDS_position",
"Protein_position", "Amino_acids", "Codons", "Existing_variation",
"Extra"
]
tsvInputRow = {
'alt_allele': '-',
'read_depth': '11572',
'ensembl_gene_id': '',
'rs_id_Variant': '',
'Platform': 'Targeted NGS',
'ucsc_gene_id': '',
'ref_allele': 'T',
'chromosome': '19',
'ncbi_gene_id': '',
'nucleotide_change': '1225delA',
'hgnc_symbol': 'KEAP1',
'consequence': 'stop gain',
'Allele_frequency': '96,47',
'Passage': '27',
'amino_acid_change': 'M409X',
'Model_ID': 'LCF16',
'datasource': 'CURIE-LC',
'ensembl_transcript_id': '',
'Sample_ID': 'LCF16p27:26/08/2016',
'seq_start_position': '10491677',
'genome_assembly': 'GRCh38',
'sample_origin': 'xenograft'
}
EMBLdf = ps.DataFrame([emblRow], columns=colNames)
NCBIdf = ps.DataFrame([ncbiRow], columns=colNames)
inputRows = ps.concat([EMBLdf, NCBIdf])
actualRow = AnnotationMerger.buildFinalTemplate(inputRows, tsvInputRow)
self.assertEquals(actualRow[20], ncbiGene)
self.assertEquals(actualRow[21], ncbiFeature)
self.assertEquals(actualRow[22], emblGene)
self.assertEquals(actualRow[23], emblFeature)