Class TestGenome
Forward strand: 1:1000-2000, strand: +, id:tr1, Protein Exons: 1:1000-1049 'exon1000', rank: 0, frame: ., sequence: tcccccccatcatagcctgaaggccccatgaataagcgtagaagacatgc 1:1100-1149 'exon1100', rank: 1, frame: ., sequence: ggctcatatgtatcgttttcgtggcttcgtacgtccgcgagtatccattg 1:1200-1249 'exon1200', rank: 2, frame: ., sequence: ctcctgaacttgtgtacctagaatacgtcggaaacaagcaatcaaccagc 1:1300-1349 'exon1300', rank: 3, frame: ., sequence: ctcccgtctccgcaggagttttcttcgtatctcacgcttctgctaatcta 1:1400-1449 'exon1400', rank: 4, frame: ., sequence: gtacggcgaatattgacaagaacggtggtatttattagaatttgcatatg 1:1500-1549 'exon1500', rank: 5, frame: ., sequence: ggtactaaagtcggaggcgggtaacgtaatcgccgcgggacgggttcagc 1:1600-1649 'exon1600', rank: 6, frame: ., sequence: tcgtaaacctaaagctataattttcacgacgctcgcaccgttcaaaaatc 1:1700-1749 'exon1700', rank: 7, frame: ., sequence: tatcgcgggttgcgtaagtttaggtatactcctggttctggattccacat 1:1800-1849 'exon1800', rank: 8, frame: ., sequence: cctaataaccagtggctccgatctggccttcttgcggcgaatttggagga 1:1900-1949 'exon1900', rank: 9, frame: ., sequence: cggctgcagcgtaaatatgtcgtttaccggggacagaaggacggaagcta CDS : tcccccccatcatagcctgaaggccccatgaataagcgtagaagacatgcggctcatatgtatcgttttcgtggcttcgtacgtccgcgagtatccattgctcctgaacttgtgtacctagaatacgtcggaaacaagcaatcaaccagcctcccgtctccgcaggagttttcttcgtatctcacgcttctgctaatctagtacggcgaatattgacaagaacggtggtatttattagaatttgcatatgggtactaaagtcggaggcgggtaacgtaatcgccgcgggacgggttcagctcgtaaacctaaagctataattttcacgacgctcgcaccgttcaaaaatctatcgcgggttgcgtaagtttaggtatactcctggttctggattccacatcctaataaccagtggctccgatctggccttcttgcggcgaatttggaggacggctgcagcgtaaatatgtcgtttaccggggacagaaggacggaagcta Protein : SPPS*PEGPMNKRRRHAAHMYRFRGFVRPRVSIAPELVYLEYVGNKQSTSLPSPQEFSSYLTLLLI*YGEY*QERWYLLEFAYGY*SRRRVT*SPRDGFSS*T*SYNFHDARTVQKSIAGCVSLGILLVLDSTS**PVAPIWPSCGEFGGRLQRKYVVYRGQKDGS?
Reverse strand: 1:1000-2000, strand: -, id:tr1, Protein Exons: 1:1000-1049 'exon1000', rank: 1000, frame: ., sequence: tcccccccatcatagcctgaaggccccatgaataagcgtagaagacatgc 1:1100-1149 'exon1100', rank: 1100, frame: ., sequence: ggctcatatgtatcgttttcgtggcttcgtacgtccgcgagtatccattg 1:1200-1249 'exon1200', rank: 1200, frame: ., sequence: ctcctgaacttgtgtacctagaatacgtcggaaacaagcaatcaaccagc 1:1300-1349 'exon1300', rank: 1300, frame: ., sequence: ctcccgtctccgcaggagttttcttcgtatctcacgcttctgctaatcta 1:1400-1449 'exon1400', rank: 1400, frame: ., sequence: gtacggcgaatattgacaagaacggtggtatttattagaatttgcatatg 1:1500-1549 'exon1500', rank: 1500, frame: ., sequence: ggtactaaagtcggaggcgggtaacgtaatcgccgcgggacgggttcagc 1:1600-1649 'exon1600', rank: 1600, frame: ., sequence: tcgtaaacctaaagctataattttcacgacgctcgcaccgttcaaaaatc 1:1700-1749 'exon1700', rank: 1700, frame: ., sequence: tatcgcgggttgcgtaagtttaggtatactcctggttctggattccacat 1:1800-1849 'exon1800', rank: 1800, frame: ., sequence: cctaataaccagtggctccgatctggccttcttgcggcgaatttggagga 1:1900-1949 'exon1900', rank: 1900, frame: ., sequence: cggctgcagcgtaaatatgtcgtttaccggggacagaaggacggaagcta CDS : cggctgcagcgtaaatatgtcgtttaccggggacagaaggacggaagctacctaataaccagtggctccgatctggccttcttgcggcgaatttggaggatatcgcgggttgcgtaagtttaggtatactcctggttctggattccacattcgtaaacctaaagctataattttcacgacgctcgcaccgttcaaaaatcggtactaaagtcggaggcgggtaacgtaatcgccgcgggacgggttcagcgtacggcgaatattgacaagaacggtggtatttattagaatttgcatatgctcccgtctccgcaggagttttcttcgtatctcacgcttctgctaatctactcctgaacttgtgtacctagaatacgtcggaaacaagcaatcaaccagcggctcatatgtatcgttttcgtggcttcgtacgtccgcgagtatccattgtcccccccatcatagcctgaaggccccatgaataagcgtagaagacatgc Protein : RLQRKYVVYRGQKDGSYLITSGSDLAFLRRIWRISRVA*V*VYSWFWIPHS*T*SYNFHDARTVQKSVLKSEAGNVIAAGRVQRTANIDKNGGIY*NLHMLPSPQEFSSYLTLLLIYS*TCVPRIRRKQAINQRLICIVFVASYVREYPLSPPS*PEGPMNKRRRH?
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Field Summary
FieldsModifier and TypeFieldDescriptionboolean
boolean
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Add markers to SnpEffPredictorvoid
checkEffect
(Variant variant, EffectType effectTypeExpected, VariantEffect.EffectImpact effectImpactExpected, int countMatchExpected) Apply a predictor to a variant and check whether the expected number of matches are foundCreate a snpEff predictor and build the forest
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Field Details
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strandMinus
public boolean strandMinus -
verbose
public boolean verbose -
config
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genomeName
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genome
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chr
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gene
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tr
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snpEffectPredictor
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markers
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Constructor Details
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TestGenome
public TestGenome(boolean strandMinus)
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Method Details
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add
Add markers to SnpEffPredictor -
checkEffect
public void checkEffect(Variant variant, EffectType effectTypeExpected, VariantEffect.EffectImpact effectImpactExpected, int countMatchExpected) Apply a predictor to a variant and check whether the expected number of matches are found -
createSnpEffectPredictor
Create a snpEff predictor and build the forest
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