diff --git a/mutalyzer/describe.py b/mutalyzer/describe.py index 520322ba07c1ff9e0cf4240393be53ab28111070..246a5d1a455efeb55841b813e4bd9b87111845c1 100644 --- a/mutalyzer/describe.py +++ b/mutalyzer/describe.py @@ -303,14 +303,13 @@ def describe_dna(s1, s2): description = Allele() in_transposition = 0 - variant_extract = extractor.extract(str(s1), len(s1), str(s2), len(s2), 0) - for variant in variant_extract.variants: - print (variant.type, variant.reference_start, - variant.reference_end, variant.sample_start, - variant.sample_end, variant.transposition_start, - variant.transposition_end) - print (variant.type & extractor.TRANSPOSITION_OPEN, variant.type & - extractor.TRANSPOSITION_CLOSE) + for variant in extractor.extract(unicode(s1), len(s1), unicode(s2), len(s2), 0): + # print (variant.type, variant.reference_start, + # variant.reference_end, variant.sample_start, + # variant.sample_end, variant.transposition_start, + # variant.transposition_end) + # print (variant.type & extractor.TRANSPOSITION_OPEN, variant.type & + # extractor.TRANSPOSITION_CLOSE) if variant.type & extractor.TRANSPOSITION_OPEN: if not in_transposition: diff --git a/mutalyzer/extractor_loader.py b/mutalyzer/extractor_loader.py index c1930c3a404abb9edbe103121b94622ec64e161e..81f43ccead409525b3c1b32b4112350e56ffc8d9 100644 --- a/mutalyzer/extractor_loader.py +++ b/mutalyzer/extractor_loader.py @@ -25,9 +25,9 @@ def main(): extracted_allele = describe.describe_dna(ref, alt) - print "Description Extractor Version " + describe.extractor.VERSION - #print "HGVS: " + describe.allele_description(extracted_allele) - print "JSON: " + json.dumps({"reference_sequence": ref, "sample_sequence": alt, "allele_description": extracted_allele}, cls=MyEncoder) + #print "Description Extractor Version " + describe.extractor.VERSION + print extracted_allele + #print "JSON: " + json.dumps({"reference_sequence": ref, "sample_sequence": alt, "allele_description": extracted_allele}, cls=MyEncoder) #main diff --git a/mutalyzer/test.py b/mutalyzer/test.py index 3bd46d1af48cebd83612dab9ffda6a191e86e911..acdca95dd7b58c417a84951d49c5ea5844c9932a 100644 --- a/mutalyzer/test.py +++ b/mutalyzer/test.py @@ -15,7 +15,6 @@ def main(): extracted_allele = describe.describe_dna(ref, alt) print extracted_allele - #print describe.allele_description(extracted_allele) print json.dumps({"reference_sequence": ref, "sample_sequence": alt, "allele_description": extracted_allele}, cls=MyEncoder) #main