diff --git a/extras/assemblies/Broad-CanFam3.1.json b/extras/assemblies/Broad-CanFam3.1.json new file mode 100644 index 0000000000000000000000000000000000000000..438f634b679ca40a9b3ef958a6d0e8fa35093176 --- /dev/null +++ b/extras/assemblies/Broad-CanFam3.1.json @@ -0,0 +1,208 @@ +{ + "name": "Broad CanFam3.1", + "alias": "canFam3", + "taxonomy_id": 9615, + "taxonomy_common_name": "Canis lupus familiaris", + "chromosomes": [ + { + "organelle": "nucleus", + "name": "chr1", + "accession": "NC_006583.3" + }, + { + "organelle": "nucleus", + "name": "chr2", + "accession": "NC_006584.3" + }, + { + "organelle": "nucleus", + "name": "chr3", + "accession": "NC_006585.3" + }, + { + "organelle": "nucleus", + "name": "chr4", + "accession": "NC_006586.3" + }, + { + "organelle": "nucleus", + "name": "chr5", + "accession": "NC_006587.3" + }, + { + "organelle": "nucleus", + "name": "chr6", + "accession": "NC_006588.3" + }, + { + "organelle": "nucleus", + "name": "chr7", + "accession": "NC_006589.3" + }, + { + "organelle": "nucleus", + "name": "chr8", + "accession": "NC_006590.3" + }, + { + "organelle": "nucleus", + "name": "chr9", + "accession": "NC_006591.3" + }, + { + "organelle": "nucleus", + "name": "chr10", + "accession": "NC_006592.3" + }, + { + "organelle": "nucleus", + "name": "chr11", + "accession": "NC_006593.3" + }, + { + "organelle": "nucleus", + "name": "chr12", + "accession": "NC_006594.3" + }, + { + "organelle": "nucleus", + "name": "chr13", + "accession": "NC_006595.3" + }, + { + "organelle": "nucleus", + "name": "chr14", + "accession": "NC_006596.3" + }, + { + "organelle": "nucleus", + "name": "chr15", + "accession": "NC_006597.3" + }, + { + "organelle": "nucleus", + "name": "chr16", + "accession": "NC_006598.3" + }, + { + "organelle": "nucleus", + "name": "chr17", + "accession": "NC_006599.3" + }, + { + "organelle": "nucleus", + "name": "chr18", + "accession": "NC_006600.3" + }, + { + "organelle": "nucleus", + "name": "chr19", + "accession": "NC_006601.3" + }, + { + "organelle": "nucleus", + "name": "chr20", + "accession": "NC_006602.3" + }, + { + "organelle": "nucleus", + "name": "chr21", + "accession": "NC_006603.3" + }, + { + "organelle": "nucleus", + "name": "chr22", + "accession": "NC_006604.3" + }, + { + "organelle": "nucleus", + "name": "chr23", + "accession": "NC_006605.3" + }, + { + "organelle": "nucleus", + "name": "chr24", + "accession": "NC_006606.3" + }, + { + "organelle": "nucleus", + "name": "chr25", + "accession": "NC_006607.3" + }, + { + "organelle": "nucleus", + "name": "chr26", + "accession": "NC_006608.3" + }, + { + "organelle": "nucleus", + "name": "chr27", + "accession": "NC_006609.3" + }, + { + "organelle": "nucleus", + "name": "chr28", + "accession": "NC_006610.3" + }, + { + "organelle": "nucleus", + "name": "chr29", + "accession": "NC_006611.3" + }, + { + "organelle": "nucleus", + "name": "chr30", + "accession": "NC_006612.3" + }, + { + "organelle": "nucleus", + "name": "chr31", + "accession": "NC_006613.3" + }, + { + "organelle": "nucleus", + "name": "chr32", + "accession": "NC_006614.3" + }, + { + "organelle": "nucleus", + "name": "chr33", + "accession": "NC_006615.3" + }, + { + "organelle": "nucleus", + "name": "chr34", + "accession": "NC_006616.3" + }, + { + "organelle": "nucleus", + "name": "chr35", + "accession": "NC_006617.3" + }, + { + "organelle": "nucleus", + "name": "chr36", + "accession": "NC_006618.3" + }, + { + "organelle": "nucleus", + "name": "chr37", + "accession": "NC_006619.3" + }, + { + "organelle": "nucleus", + "name": "chr38", + "accession": "NC_006620.3" + }, + { + "organelle": "nucleus", + "name": "chrX", + "accession": "NC_006621.3" + }, + { + "organelle": "mitochondrion", + "name": "chrM", + "accession": "NC_002008.4" + } + ] +} diff --git a/mutalyzer/Retriever.py b/mutalyzer/Retriever.py index e514ab96bc3a0cd1519513acaedde13afcb9c584..ad0165b5c35a82dfc1c8694dfd9af90f3295302a 100644 --- a/mutalyzer/Retriever.py +++ b/mutalyzer/Retriever.py @@ -404,6 +404,11 @@ class GenBankRetriever(Retriever): 'Could not retrieve %s.' % name) return None + if b'Resource temporarily unavailable' in raw_data: + self._output.addMessage(__file__, 4, 'ERETR', + 'Resource temporarily unavailable from NCBI servers: %s.' % name) + return None + # This is a hack to detect constructed references, the proper way to # do this would be to check the data_file_division attribute of the # parsed GenBank file (it would be 'CON'). diff --git a/tests/test_variantchecker.py b/tests/test_variantchecker.py index d82e9c83137d6bd9055a5b1bcd9f4710731bd55b..735ff27b7881fc6371aca89ee4036697e80d8678 100644 --- a/tests/test_variantchecker.py +++ b/tests/test_variantchecker.py @@ -1284,7 +1284,7 @@ class TestVariantchecker(MutalyzerTest): wnomrna_other = self.output.getMessagesWithErrorCode('WNOMRNA_OTHER') assert len(wnomrna_other) == 1 - @fix(cache('A1BG')) + @fix(cache('AF230870.1')) def test_wnomrna(self): """ Warning for no mRNA field on currently selected transcript should give