def test_variable_stratified_mapping_plus(self):
offsets = {
26 : 6,
27 : 22,
28 : 13,
29 : 4,
30 : 5
}
chains = {
"fw" : SegmentChain(GenomicSegment('chrII',392959,393180,'+'),
GenomicSegment('chrII',393510,394742,'+'),
GenomicSegment('chrII',394860,394901,'+'),
ID='YBR078W_mRNA'),
"rc" : SegmentChain(GenomicSegment('chrVIII',189061,189749,'-'),
GenomicSegment('chrVIII',189850,190017,'-'),
ID='YHR041C_mRNA')
}
expected = {
"fw" : numpy.loadtxt(resource_filename("plastid","test/data/stratmap/strat_fw_vec.txt"),delimiter="\t"),
"rc" : numpy.loadtxt(resource_filename("plastid","test/data/stratmap/strat_rc_vec.txt"),delimiter="\t"),
}
ga = BAMGenomeArray([resource_filename("plastid","test/data/stratmap/strat.bam")])
ga.set_mapping(StratifiedVariableFivePrimeMapFactory(offsets,26,30))
