TestCasesAlign |
test cases for Sequence alignment
|
TestCasesAnnParse |
Test case for parsing ANN fields
|
TestCasesApplyDel |
Test cases: apply a variant (DEL) to a transcript
|
TestCasesApplyIns |
Test cases: apply a variant (INS) to a transcript
|
TestCasesApplyMixed |
Test cases: apply a variant (MIXED) to a transcript
|
TestCasesApplyMnp |
Test cases: apply a variant (MNP) to a transcript
|
TestCasesApplySnp |
Test cases: apply a variant (SNP) to a transcript
|
TestCasesBase |
Base class for some test cases
|
TestCasesBaseApply |
Test case
Transcript:
1:0-999, strand: +, id:transcript1, Protein
Exons:
1:100-199 'exon1', rank: 1, frame: ., sequence: atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg
1:300-399 'exon2', rank: 2, frame: ., sequence: tgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg
1:900-999 'exon3', rank: 0, frame: ., sequence: ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg
CDS : atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatggtgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacgggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg
Protein : MSAGEGIHAARILMLPRWILSEIWCPGREGHIMVFGNSRARFCSKLNWQLGINPDPIVTHGSIHPQRVEEKHLTPIEQDLFRNTLYRLPIYLIPHIYFIG
Transcript (full coordinates):
0
0 1 2 3 4 5 6 7 8 9
0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9
0123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789
....................................................................................................atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg....................................................................................................tgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg
M S A G E G I H A A R I L M L P R W I L S E I W C P G R E G H I M V F G N S R A R F C S K L N W Q L G I N P D P I V T H G S I H P Q R V E E K H L T P I E Q D L F R N T L Y R L P I Y L I P H I Y F I G
0120120120120120120120120120120120120120120120120120120120120120120120120120120120120120120120120120 1201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201 2012012012012012012012012012012012012012012012012012012012012012012012012012012012012012012012012012
---------------------------------------------------------------------------------------------------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>---------------------------------------------------------------------------------------------------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
| | | | | |
| | | | | |^999
| | | | |^900
| | | |^399
| | |^300
| |^199
|^100
|
TestCasesBinomial |
Test for Binomial distribution
|
TestCasesBuild |
Test case
|
TestCasesCds |
Test random SNP changes
|
TestCasesChiSquare |
Test for Hypergeometric distribution and Fisher exact test
|
TestCasesCircular |
Test cases for circular genomes
|
TestCasesCochranArmitage |
Cochran-Armitage test statistic test case
|
TestCasesCodonTable |
Codon tables
|
TestCasesCytoBands |
Test case for cytobands
|
TestCasesDel |
Test random DEL changes
|
TestCasesDels |
Test random DEL changes
|
TestCasesDnaNSequence |
|
TestCasesDnaOverlap |
|
TestCasesDnaSequence |
|
TestCasesDnaSequenceByte |
|
TestCasesEffectCollapse |
Test Splice sites variants
The sample transcript used is:
Transcript:1:751-1139, strand: +, id:transcript_0, Protein
Exons:
1:751-810 'exon_0_0', rank: 1, frame: ., sequence: cgattgacctacatagtaatgagttttgttggtccgtaagacttcgcccaaaaccgcgca
1:1013-1139 'exon_0_1', rank: 2, frame: ., sequence: cttcgactactcgggggtctaagcacgttttctgcagggaaagtaatatatgcttgtgcgcaaccatggtaacagggattcacggccccgttaatggtatgacctaagccccatacgagtcatccaa
CDS : cgattgacctacatagtaatgagttttgttggtccgtaagacttcgcccaaaaccgcgcacttcgactactcgggggtctaagcacgttttctgcagggaaagtaatatatgcttgtgcgcaaccatggtaacagggattcacggccccgttaatggtatgacctaagccccatacgagtcatccaa
Protein : RLTYIVMSFVGP*DFAQNRALRLLGGLSTFSAGKVIYACAQPW*QGFTAPLMV*PKPHTSHP?
|
TestCasesEffectCollapse2 |
Test case
|
TestCasesFasta |
Test case for FASTA file parsing
|
TestCasesFileIndexChrPos |
Test cases for file index (chr:pos index on files)
|
TestCasesFisherExactTest |
Test for Hypergeometric distribution and Fisher exact test
|
TestCasesGenePvalueList |
GenePvalueList statistics test case
|
TestCasesGenomicSequences |
Test case
|
TestCasesGenotypeVector |
Test cases for GenotypeVector class
|
TestCasesHgvs |
Test case for basic HGV annotaions
|
TestCasesHgvsDnaDup |
Test case
|
TestCasesHgvsDnaDupNegative |
Test cases for HGVS's 'dup' on the negative strand
|
TestCasesHgvsProtDup |
Test case
|
TestCasesHypergeometric |
Test for Hypergeometric distribution and Fisher exact test
|
TestCasesIns |
Test random SNP changes
|
TestCasesIntergenic |
Test intergenic markers
|
TestCasesIntervals |
|
TestCasesIntervalTree |
Test case for interval tree structure
|
TestCasesIntervalTreeArray |
Test case for interval tree structure
|
TestCasesIntervalTreeOri |
Test case for interval tree structure
|
TestCasesIntervalVariant |
Test random Interval Variants (e.g.
|
TestCasesIntStats |
|
TestCasesIubString |
|
TestCasesJaspar |
Test case for Jaspar parsing
|
TestCasesMarkerUtils |
|
TestCasesMnps |
Test random SNP changes
|
TestCasesNmers |
|
TestCasesOverlap |
|
TestCasesProteinInteraction |
Test cases for protein interaction
|
TestCasesReactome |
Test Reactome circuits
|
TestCasesSeekableReader |
Seekable file reader test case
|
TestCasesSequenceIndexer |
|
TestCasesSnps |
Test random SNP changes
|
TestCasesSpliceRegion |
Test Splice sites variants
|
TestCasesSpliceSite |
Test Splice sites variants
|
TestCasesStructuralDel |
Test case
Gene: geneId1
1:957-1157, strand: +, id:transcript_0, Protein
Exons:
1:957-988 'exon_0_0', rank: 1, frame: ., sequence: gttgcttgaatactgtatagccttgccattgt
1:1045-1057 'exon_0_1', rank: 2, frame: ., sequence: tgtgttgctaact
1:1148-1157 'exon_0_2', rank: 3, frame: ., sequence: agacatggac
CDS : gttgcttgaatactgtatagccttgccattgttgtgttgctaactagacatggac
Protein : VA*ILYSLAIVVLLTRHG?
1
0 1
6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5
789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567
gttgcttgaatactgtatagccttgccattgt........................................................tgtgttgctaact..........................................................................................agacatggac
V A * I L Y S L A I V V L L T R H G
01201201201201201201201201201201 2012012012012 0120120120
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>-------------------------------------------------------->>>>>>>>>>>>>------------------------------------------------------------------------------------------>>>>>>>>>>
| | | | | |
| | | | | ^1157
| | | | ^1148
| | | ^1057
| | ^1045
| ^988
^957
Gene: geneId2
1:2066-2141, strand: +, id:transcript_1, Protein
Exons:
1:2066-2069 'exon_1_0', rank: 1, frame: ., sequence: actt
1:2084-2089 'exon_1_1', rank: 2, frame: ., sequence: cccttt
1:2116-2126 'exon_1_2', rank: 3, frame: ., sequence: tacgcccacgt
1:2133-2141 'exon_1_3', rank: 4, frame: ., sequence: ccgccgctg
CDS : acttcccttttacgcccacgtccgccgctg
Protein : TSLLRPRPPL
1
7 8 9 0 1 2 3 4
6789012345678901234567890123456789012345678901234567890123456789012345678901
actt..............cccttt..........................tacgcccacgt......ccgccgctg
T S L L R P R P P L
0120 120120 12012012012 012012012
>>>>-------------->>>>>>-------------------------->>>>>>>>>>>------>>>>>>>>>
| | | | | | | |
| | | | | | | ^2141
| | | | | | ^2133
| | | | | ^2126
| | | | ^2116
| | | ^2089
| | ^2084
| ^2069
^2066
|
TestCasesStructuralDup |
Test case for structural variants: Duplications
|
TestCasesStructuralInv |
Test cases for structural variants: Inversions
Gene models used in these test cases:
Gene: Gene_1:953-1216
1:957-1157, strand: +, id:transcript_0, Protein
Exons:
1:957-988 'exon_0_0', rank: 1, frame: ., sequence: gttgcttgaatactgtatagccttgccattgt
1:1045-1057 'exon_0_1', rank: 2, frame: ., sequence: tgtgttgctaact
1:1148-1157 'exon_0_2', rank: 3, frame: ., sequence: agacatggac
CDS : gttgcttgaatactgtatagccttgccattgttgtgttgctaactagacatggac
Protein : VA*ILYSLAIVVLLTRHG?
1
0 1
6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5
789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567
gttgcttgaatactgtatagccttgccattgt........................................................tgtgttgctaact..........................................................................................agacatggac
V A * I L Y S L A I V V L L T R H G
01201201201201201201201201201201 2012012012012 0120120120
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>-------------------------------------------------------->>>>>>>>>>>>>------------------------------------------------------------------------------------------>>>>>>>>>>
| | | | | |
| | | | | ^1157
| | | | ^1148
| | | ^1057
| | ^1045
| ^988
^957
Gene: Gene_1:2057-2157
1:2066-2141, strand: +, id:transcript_1, Protein
Exons:
1:2066-2069 'exon_1_0', rank: 1, frame: ., sequence: actt
1:2084-2089 'exon_1_1', rank: 2, frame: ., sequence: cccttt
1:2116-2126 'exon_1_2', rank: 3, frame: ., sequence: tacgcccacgt
1:2133-2141 'exon_1_3', rank: 4, frame: ., sequence: ccgccgctg
CDS : acttcccttttacgcccacgtccgccgctg
Protein : TSLLRPRPPL
1
7 8 9 0 1 2 3 4
6789012345678901234567890123456789012345678901234567890123456789012345678901
actt..............cccttt..........................tacgcccacgt......ccgccgctg
T S L L R P R P P L
0120 120120 12012012012 012012012
>>>>-------------->>>>>>-------------------------->>>>>>>>>>>------>>>>>>>>>
| | | | | | | |
| | | | | | | ^2141
| | | | | | ^2133
| | | | | ^2126
| | | | ^2116
| | | ^2089
| | ^2084
| ^2069
^2066
|
TestCasesStructuralTranslocations |
Test case for structural variants: Translocation (fusions)
We create two genes (one transcript each).
|
TestCasesVariantDecompose |
Test cases: apply a variant (MIXED) to a transcript
|
TestCasesVariantRealignment |
Test cases for variant realignment
|
TestCasesVcf |
VCF parsing test cases
|
TestCasesZzz |
Test random SNP changes
|