예제 #1
0
    def setUp(self):
        self.reference_set = ReferenceSet().create_and_save(name="ref_set")
        self.variant_set = VariantSet.create_and_save(
            name="this_vcf_file2",
            reference_set=self.reference_set)
        self.variant_sets = [self.variant_set]
        self.reference = Reference().create_and_save(
            name="ref",
            md5checksum="sre",
            reference_sets=[
                self.reference_set])
        self.call_set = VariantCallSet.create(
            sample_id="C00123",
            name="C00123",
            variant_sets=self.variant_sets)
        self.variant_snp = Variant.create(variant_sets=self.variant_sets,
                                          start=0, end=1, reference_bases="A",
                                          alternate_bases=["T"],
                                          reference=self.reference)

        self.variant_snp_mult_alts = Variant.create(
            variant_sets=self.variant_sets,
            start=0,
            end=1,
            reference_bases="T",
            alternate_bases=[
                "A",
                "C"],
            reference=self.reference)
예제 #2
0
 def setUp(self):
     DB.drop_database('atlas-test')
     self.reference_set = ReferenceSet().create_and_save(name="ref_set")
     self.reference = Reference().create_and_save(
         name="NC_000962.3",
         md5checksum="sre",
         reference_sets=[self.reference_set])
예제 #3
0
 def setUp(self):
     DB.drop_database('ga4ghmongo-test')
     self.reference_set = ReferenceSet().create_and_save(name="ref_set")
     self.variant_set = VariantSet.create_and_save(
         name="this_vcf_file", reference_set=self.reference_set)
     self.variant_sets = [self.variant_set]
     self.reference = Reference().create_and_save(
         name="ref", md5checksum="sre", reference_sets=[self.reference_set])
예제 #4
0
 def setUp(self):
     DB.drop_database('atlas-test')
     self.pg = AlleleGenerator(
         reference_filepath="atlasvar/data/NC_000962.2.fasta")
     self.reference_set = ReferenceSet().create_and_save(name="ref_set")
     self.variant_set = VariantSet.create_and_save(
         name="this_vcf_file", reference_set=self.reference_set)
     self.variant_sets = [self.variant_set]
     self.reference = Reference().create_and_save(
         name="ref", md5checksum="sre", reference_sets=[self.reference_set])
예제 #5
0
 def setUp(self):
     DB.drop_database('atlas-test')
     self.reference_set = ReferenceSet().create_and_save(name="ref_set")
     self.reference = Reference().create_and_save(
         name="NC_000962.3",
         md5checksum="sre",
         reference_sets=[self.reference_set])
     vcf = VCF(f="tests/vcf_tests/test.vcf",
               reference_set_id=self.reference_set.id,
               method="CORTEX")
     vcf.add_to_database()
예제 #6
0
 def setUp(self):
     DB.drop_database('atlas-test')
     with open("mykatlas/data/NC_000962.3.fasta", 'r') as infile:
         self.reference_seq = list(SeqIO.parse(infile, "fasta"))[0].seq
     self.gm = GeneAminoAcidChangeToDNAVariants(
         reference="mykatlas/data/NC_000962.3.fasta",
         genbank="mykatlas/data/NC_000962.3.gb")
     self.reference_set = ReferenceSet().create_and_save(name="ref_set")
     self.variant_set = VariantSet.create_and_save(
         name="this_vcf_file", reference_set=self.reference_set)
     self.variant_sets = [self.variant_set]
     self.reference_id = Reference().create_and_save(
         name="ref", md5checksum="sre", reference_sets=[self.reference_set])