diff --git a/mutalyzer/extractor_loader.py b/mutalyzer/extractor_loader.py new file mode 100644 index 0000000000000000000000000000000000000000..7401efd3a34d1c0977f60697f46b3d56d08ef70a --- /dev/null +++ b/mutalyzer/extractor_loader.py @@ -0,0 +1,35 @@ +#!/usr/bin/env python + +import sys + +import json + +import describe + +class MyEncoder(json.JSONEncoder): + def default(self, o): + return o.__dict__ + +def main(): + if len(sys.argv) < 3: + print "usage: " + sys.argv[0] + " reference sample" + exit() + #if + + f = open(sys.argv[1], "r") + ref = f.read() + f.close() + f = open(sys.argv[2], "r") + alt = f.read() + f.close() + + extracted_allele = describe.describe(ref, alt) + + print 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) + +#main + +if __name__ == "__main__": + main() diff --git a/mutalyzer/test.py b/mutalyzer/test.py new file mode 100644 index 0000000000000000000000000000000000000000..d49390252fc65252d2fa787feeba0a7857c46caf --- /dev/null +++ b/mutalyzer/test.py @@ -0,0 +1,24 @@ +#!/usr/bin/env python + +import json + +import describe + +class MyEncoder(json.JSONEncoder): + def default(self, o): + return o.__dict__ + +def main(): + ref = "ACGTCGATTCGCTAGCTTCGGGGGATAGATAGAGATATAGAGATATTTTT" + alt = "ACGTCGGTTCGCTAGCTTCGGGGGATAGATAGATATATAGAGATATTTTT" + + extracted_allele = describe.describe(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 + +if __name__ == "__main__": + main()