Class TestGenome
- java.lang.Object
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- org.snpeff.snpEffect.testCases.unity.TestGenome
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public class TestGenome extends java.lang.Object
Creates a simple "genome" for testing: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
Fields Modifier and Type Field Description Chromosome
chr
Config
config
Gene
gene
Genome
genome
java.lang.String
genomeName
Markers
markers
SnpEffectPredictor
snpEffectPredictor
boolean
strandMinus
Transcript
tr
boolean
verbose
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Constructor Summary
Constructors Constructor Description TestGenome(boolean strandMinus)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
add(Marker marker)
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 foundSnpEffectPredictor
createSnpEffectPredictor()
Create a snpEff predictor and build the forest
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Field Detail
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strandMinus
public boolean strandMinus
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verbose
public boolean verbose
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config
public Config config
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genomeName
public java.lang.String genomeName
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genome
public Genome genome
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chr
public Chromosome chr
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gene
public Gene gene
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tr
public Transcript tr
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snpEffectPredictor
public SnpEffectPredictor snpEffectPredictor
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markers
public Markers markers
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Method Detail
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add
public void add(Marker marker)
Add markers to SnpEffPredictor
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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
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createSnpEffectPredictor
public SnpEffectPredictor createSnpEffectPredictor()
Create a snpEff predictor and build the forest
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