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 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 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 test_closest_transcript_to_peak(self): features = FeatureSet('Transcripts-ex1.txt') feature1 = features[1] feature2 = features[2] peaks = PeakSet('ChIP_peaks-ex1.txt') peak = peaks[0] nearest = GetNearestTranscriptToPeak(feature1, feature2, peak) # 2nd feature should be closer than first self.assertEqual(nearest, feature1, "Wrong transcript selected as nearest") # test when only one is set nearest = GetNearestTranscriptToPeak(None, feature2, peak) self.assertEqual(nearest, feature2, "Wrong transcript selected as nearest")