def test_write_features_summary(self): # Set up some test data peak = Peak('chr2L',66811,66812) features = FeatureSet( features_list=( Feature('CG31973','chr2L',25402,59243,'-'), Feature('CG2674-RE','chr2L',106903,114433,'+'), Feature('CG2674-RC','chr2L',107926,114433,'+'))) # Temp output file fp,summary = tempfile.mkstemp() # Write peaks to file ap = AnalysisReportWriter(output.MULTI_LINE, fields=('peak.chr', 'peak.start', 'peak.end', 'order', 'feature.id', 'dist_closest', 'dist_TSS'), summary=summary) ap.write_nearest_features(peak,features) ap.close() # Expected and actual output expected_output = \ "#peak.chr\tpeak.start\tpeak.end\torder\tfeature.id\tdist_closest\tdist_TSS\n" \ "chr2L\t66811\t66812\t1 of 3\tCG31973\t7568\t7568\n" actual_output = open(summary,'r').read() # Check that output matches self.assertEqual(expected_output,actual_output)
def test_tss_distances_peak_contains_TSS(self): self.assertEqual( tss_distances(Peak('chr1', '100', '250'), Feature('NM3', 'chr1', '200', '400', '+')), (0, 75)) self.assertEqual( tss_distances(Peak('chr1', '250', '350'), Feature('NM4', 'chr1', '200', '300', '-')), (0, 50))
def setUp(self): # Set up some test data self.peak = Peak('chr2L',66811,66812) self.features = FeatureSet( features_list=( Feature('CG31973','chr2L',25402,59243,'-'), Feature('CG2674-RE','chr2L',106903,114433,'+'), Feature('CG2674-RC','chr2L',107926,114433,'+'))) self.single_line_fields = ('peak.chr', 'peak.start', 'peak.end', 'number_of_results', 'list(feature.id,' 'dist_closest,dist_TSS)') self.single_line_fields_extra_data = ('peak.chr', 'peak.start', 'peak.end', 'cutoff', 'number_of_results', 'list(feature.id,' 'dist_closest,dist_TSS)') self.multi_line_fields = ('peak.chr', 'peak.start', 'peak.end', 'order', 'feature.id', 'dist_closest', 'dist_TSS')
def setUp(self): # Set up Feature objects to be used in the tests # Forward strand example self.rna_data = \ Feature('CG9130-RB','chr3L','1252012','1255989','+') # Reverse strand example self.rna_data_2 = \ Feature('CG13051-RA','chr3L','16257914','16258166','-')
def test_tss_distances_TSS_before_peak(self): self.assertEqual( tss_distances(Peak('chr1', '250', '400'), Feature('NM2', 'chr1', '100', '200', '+')), (150, 300)) self.assertEqual( tss_distances(Peak('chr1', '250', '400'), Feature('NM2', 'chr1', '100', '200', '-')), (50, 200))
def test_write_peaks_summary(self): # Set up some test data feature = Feature('CG31973','chr2L','25402','59243','-') peaks = PeakSet( peaks_list=( Peak('chr2L','66711','66911'), Peak('chr2L','249077','249277'), Peak('chr2L','605850','606050'))) # Temp output files fp,summary= tempfile.mkstemp() # Write peaks to file ap = AnalysisReportWriter(output.MULTI_LINE, fields=('feature.id', 'order', 'peak.chr', 'peak.start', 'peak.end', 'dist_closest', 'dist_TSS'), summary=summary) ap.write_nearest_peaks(feature,peaks) ap.close() # Expected and actual output expected_output = \ "#feature.id\torder\tpeak.chr\tpeak.start\tpeak.end\tdist_closest\tdist_TSS\n" \ "CG31973\t1 of 3\tchr2L\t66711\t66911\t7468\t7468\n" actual_output = open(summary,'r').read() # Check that output matches self.assertEqual(expected_output,actual_output)
def test_write_features_append(self): # Set up some test data peak = Peak('chr2L',66811,66812) features1 = FeatureSet( features_list=( Feature('CG31973','chr2L',25402,59243,'-'), Feature('CG2674-RE','chr2L',106903,114433,'+'),)) features2 = FeatureSet( features_list=( Feature('CG2674-RC','chr2L',107926,114433,'+'),)) # Temp output file fp,outfile = tempfile.mkstemp() # Write first set of nearest features ap = AnalysisReportWriter(output.MULTI_LINE, fields=('peak.chr', 'peak.start', 'peak.end', 'order', 'feature.id', 'dist_closest', 'dist_TSS'), outfile=outfile) ap.write_nearest_features(peak,features1) ap.close() # Write second set of nearest features ap = AnalysisReportWriter(output.MULTI_LINE, fields=('peak.chr', 'peak.start', 'peak.end', 'order', 'feature.id', 'dist_closest', 'dist_TSS'), outfile=outfile, append=True) ap.write_nearest_features(peak,features2) ap.close() # Expected and actual output expected_output = \ "#peak.chr\tpeak.start\tpeak.end\torder\tfeature.id\tdist_closest\tdist_TSS\n" \ "chr2L\t66811\t66812\t1 of 2\tCG31973\t7568\t7568\n" \ "chr2L\t66811\t66812\t2 of 2\tCG2674-RE\t40091\t40091\n" \ "chr2L\t66811\t66812\t1 of 1\tCG2674-RC\t41114\t41114\n" actual_output = open(outfile,'r').read() # Check that output matches self.assertEqual(expected_output,actual_output)
def setUp(self): # Set up some test data self.feature = Feature('CG31973','chr2L','25402','59243','-') self.peaks = PeakSet( peaks_list=( Peak('chr2L','66711','66911'), Peak('chr2L','249077','249277'), Peak('chr2L','605850','606050'))) self.single_line_fields = ('feature.id', 'number_of_results', 'list(peak.chr,peak.start,peak.end,' 'dist_closest,dist_TSS)') self.single_line_fields_extra_data = ('feature.id', 'cutoff', 'number_of_results', 'list(peak.chr,peak.start,peak.end,' 'dist_closest,dist_TSS)') self.multi_line_fields = ('feature.id', 'order', 'peak.chr', 'peak.start', 'peak.end', 'dist_closest', 'dist_TSS')
def test_feature_upstream_from_peak_neg_strand(self): peak = Peak('chr1', '100', '200') feature = Feature('NM1', 'chr1', '250', '400', '-') self.assertEqual(direction(peak, feature), UPSTREAM)
def test_feature_downstream_from_peak(self): peak = Peak('chr1', '100', '200') feature = Feature('NM1', 'chr1', '250', '400', '+') self.assertEqual(direction(peak, feature), DOWNSTREAM)
def test_feature_upstream_from_peak_partial_overlap(self): peak = Peak('chr1', '350', '550') feature = Feature('NM1', 'chr1', '250', '400', '+') self.assertEqual(direction(peak, feature), UPSTREAM)
def test_peak_downstream_from_feature_neg_strand(self): peak = Peak('chr1', '450', '550') feature = Feature('NM1', 'chr1', '250', '400', '-') self.assertEqual(direction(feature, peak), UPSTREAM)
def test_peak_upstream_from_feature_neg_strand_partial_overlap(self): peak = Peak('chr1', '100', '300') feature = Feature('NM1', 'chr1', '250', '400', '-') self.assertEqual(direction(feature, peak), DOWNSTREAM)
def test_peak_downstream_from_feature_partial_overlap(self): peak = Peak('chr1', '350', '550') feature = Feature('NM1', 'chr1', '250', '400', '+') self.assertEqual(direction(feature, peak), DOWNSTREAM)
def test_peak_full_overlap_feature(self): peak = Peak('chr1', '200', '450') feature = Feature('NM1', 'chr1', '250', '400', '+') self.assertEqual(direction(feature, peak), OVERLAP)
class TestFeature(unittest.TestCase): def setUp(self): # Set up Feature objects to be used in the tests # Forward strand example self.rna_data = \ Feature('CG9130-RB','chr3L','1252012','1255989','+') # Reverse strand example self.rna_data_2 = \ Feature('CG13051-RA','chr3L','16257914','16258166','-') def test_properties(self): self.assertEqual(self.rna_data.chrom,'chr3L') self.assertEqual(self.rna_data_2.chrom,'chr3L') def test__eq__(self): self.assertEqual(self.rna_data,Feature('CG9130-RB', 'chr3L', '1252012', '1255989','+')) self.assertNotEqual(self.rna_data,self.rna_data_2) def test_contains_position(self): position = 1253000 self.assertTrue(self.rna_data.containsPosition(position), "Transcript should contain position") position = 4250000 self.assertFalse(self.rna_data.containsPosition(position), "Transcript should not contain position") position = 10000 self.assertFalse(self.rna_data.containsPosition(position), "Transcript should not contain position") def test_get_closest_edge_distance(self): # Single position position = 1200000 # Single reference position self.assertEqual(self.rna_data.getClosestEdgeDistanceTo(position), abs(self.rna_data.start-position), "Incorrect closest edge distance #1") position = 1300000 self.assertEqual(self.rna_data.getClosestEdgeDistanceTo(position), abs(self.rna_data.end-position), "Incorrect closest edge distance #2") def test_get_closest_edge_distance_outside_region(self): # Reference region (2 positions) position1 = 1100000 position2 = 1200000 self.assertEqual(self.rna_data.getClosestEdgeDistanceTo(position1, position2), abs(self.rna_data.start-position2), "Incorrect closest edge distance (region #1)") position1 = 1300000 position2 = 1400000 self.assertEqual(self.rna_data.getClosestEdgeDistanceTo(position1, position2), abs(self.rna_data.end-position1), "Incorrect closest edge distance (region #2)") def test_get_closest_edge_distance_partially_inside_region(self): # Partially inside reference region position1 = 1200000 position2 = 1255000 self.assertEqual(self.rna_data.getClosestEdgeDistanceTo(position1, position2), abs(self.rna_data.end-position2), "Incorrect closest edge distance (inside region #1)") self.assertEqual(self.rna_data.getClosestEdgeDistanceTo(position1, position2, zero_inside_region=True), 0, "Incorrect closest edge distance (inside region #2)") def test_get_closest_edge_distance_completely_inside_region(self): # Completely inside reference region position1 = 1250000 position2 = 1300000 self.assertEqual(self.rna_data.getClosestEdgeDistanceTo(position1, position2), abs(self.rna_data.start-position1), "Incorrect closest edge distance (inside region #3)") self.assertEqual(self.rna_data.getClosestEdgeDistanceTo(position1, position2, zero_inside_region=True), 0, "Incorrect closest edge distance (inside region #4)") def test_get_promoter_region(self): leading = 10000 trailing = 2500 promoter = self.rna_data.getPromoterRegion(leading,trailing) self.assertEqual(promoter, (self.rna_data.getTSS()-leading, self.rna_data.getTSS()+trailing), "Incorrect promoter region for + strand example") promoter = self.rna_data_2.getPromoterRegion(leading,trailing) self.assertEqual(promoter, (self.rna_data_2.getTSS()+leading, self.rna_data_2.getTSS()-trailing), "Incorrect promoter region for - strand example")
def test_feature_downstream_from_peak_neg_strand_partial_overlap(self): peak = Peak('chr1', '350', '550') feature = Feature('NM1', 'chr1', '250', '400', '-') self.assertEqual(direction(peak, feature), DOWNSTREAM)
def test_distances_feature_before_peak(self): self.assertEqual( edge_distances(Peak('chr1', '250', '400'), Feature('NM2', 'chr1', '100', '200', '+')), (50, 150))
def test_distances_feature_contains_peak(self): self.assertEqual( edge_distances(Peak('chr1', '250', '350'), Feature('NM6', 'chr1', '100', '400', '+')), (0, 0))
def test_distances_feature_overlaps_peak_start(self): self.assertEqual( edge_distances(Peak('chr1', '250', '350'), Feature('NM4', 'chr1', '300', '400', '+')), (0, 50))
def test_feature_full_overlap_peak_neg_strand(self): peak = Peak('chr1', '200', '450') feature = Feature('NM1', 'chr1', '250', '400', '-') self.assertEqual(direction(peak, feature), OVERLAP)
def test_peak_upstream_from_feature(self): peak = Peak('chr1', '100', '200') feature = Feature('NM1', 'chr1', '250', '400', '+') self.assertEqual(direction(feature, peak), UPSTREAM)