diff --git a/mutalyzer/variant.py b/mutalyzer/variant.py index 33ffc25854e5b3d0e16a2c6adfe9a058b0aa09b0..a8e512a255dbad2319f0617d744d27c031652916 100644 --- a/mutalyzer/variant.py +++ b/mutalyzer/variant.py @@ -70,6 +70,9 @@ class ISeq(object): if self.type == "ins": return self.sequence + if not (self.start or self.end): + return "" + inverted = "inv" if self.reverse else "" return "{}_{}{}".format(self.start, self.end, inverted) #__str__ diff --git a/mutalyzer/website/views.py b/mutalyzer/website/views.py index c1d761c4b00d76812cf607a18b30fcca9bd27d19..5bb2ae3576c049e40ad7968aebc1fe8550041f87 100644 --- a/mutalyzer/website/views.py +++ b/mutalyzer/website/views.py @@ -269,14 +269,18 @@ def name_checker(): # Experimental description extractor. if (output.getIndexedOutput('original', 0) and output.getIndexedOutput('mutated', 0)): - extracted = extractedProt = '(skipped)' + allele = describe.describe_dna(output.getIndexedOutput('original', 0), + output.getIndexedOutput('mutated', 0)) + #prot_allele = describe.describe_protein( + # output.getIndexedOutput('oldprotein', 0), + # output.getIndexedOutput('newprotein', 0, default='')) + prot_allele = '' - allele = describe.describe(output.getIndexedOutput('original', 0), - output.getIndexedOutput('mutated', 0)) + extracted = extractedProt = '(skipped)' if allele: - extracted = describe.allele_description(allele) + extracted = str(allele) #describe.allele_description(allele) if prot_allele: - extractedProt = describe.allele_description(prot_allele) + extractedProt = str(prot_allele) #describe.allele_description(prot_allele) else: extracted = extractedProt = '' @@ -695,8 +699,8 @@ def description_extractor(): output.addMessage(__file__, 3, 'ENODNA', 'Variant sequence is not DNA.') - raw_vars = describe.describe(reference_sequence, variant_sequence) - description = describe.allele_description(raw_vars) + raw_vars = describe.describe_dna(reference_sequence, variant_sequence) + description = str(raw_vars) #describe.allele_description(raw_vars) errors, warnings, summary = output.Summary() messages = map(util.message_info, output.getMessages()) diff --git a/tests/test_describe.py b/tests/test_describe.py index 2ef7db3de4690cc97903f3239fa1cd0f9b9a496d..c65e57a599929f35da57bcb5842fc194ce58a938 100644 --- a/tests/test_describe.py +++ b/tests/test_describe.py @@ -16,7 +16,7 @@ from utils import MutalyzerTest class TestDescribe(MutalyzerTest): """ - Test the mytalyzer.describe module. + Test the mutalyzer.describe module. """ def _single_variant(self, sample, expected):