class TestMutation():
def setup(self):
self.reference_filepath = "src/mykrobe/data/NC_000962.3.fasta"
self.reference = os.path.basename(
self.reference_filepath).split('.fa')[0]
self.aa2dna = GeneAminoAcidChangeToDNAVariants(
"src/mykrobe/data/NC_000962.3.fasta",
"src/mykrobe/data/NC_000962.3.gb")
def teardown(self):
pass
def test_mutation_name_forward_strand(self):
gene = "rpoB"
mutation_string = "S450L"
is_protein_coding_var = True
assert set(
self.aa2dna.get_variant_names(gene, mutation_string,
is_protein_coding_var)) == set([
"TCG761154TTA", "TCG761154TTG",
"TCG761154CTA", "TCG761154CTT",
"TCG761154CTC", "TCG761154CTG"
])
mutation = Mutation(reference=self.reference,
var_name="TCG761154TTA",
gene=self.aa2dna.get_gene("rpoB"),
mut="S450L")
assert mutation.mutation_output_name == "S450L"
def test_mutation_name_reverse_strand(self):
gene = "gid"
mutation_string = "I11N"
is_protein_coding_var = True
assert set(
self.aa2dna.get_variant_names(gene, mutation_string,
is_protein_coding_var)) == set([
"GAT4408170ATT", "GAT4408170GTT"
])
mutation = Mutation(reference=self.reference,
var_name="GAT4408170ATT",
gene=self.aa2dna.get_gene("gid"),
mut="I11N")
assert mutation.mutation_output_name == "I11N"
def test_mutation_name_dna_space(self):
gene = "pncA"
mutation_string = "C18CCA"
is_protein_coding_var = False
assert set(
self.aa2dna.get_variant_names(gene, mutation_string,
is_protein_coding_var)) == set(
["G2289224TGG"])
mutation = Mutation(reference=self.reference,
var_name=self.aa2dna.get_variant_names(
gene, mutation_string,
is_protein_coding_var)[0],
gene=self.aa2dna.get_gene(gene),
mut=mutation_string)
assert mutation.mutation_output_name == "C18CCA"
class TestRegions():
def teardown(self):
DB.drop_database('mykrobe-test')
def setup(self):
DB.drop_database('mykrobe-test')
with open("src/mykrobe/data/NC_000962.3.fasta", 'r') as infile:
self.reference_seq = list(SeqIO.parse(infile, "fasta"))[0].seq
self.gm = GeneAminoAcidChangeToDNAVariants(
reference="src/mykrobe/data/NC_000962.3.fasta",
genbank="src/mykrobe/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])
def test_simple_gene(self):
g = Gene(name="rpoB",
reference=self.reference_seq,
start=759807,
end=763325)
assert g.name == "rpoB"
assert g.forward
assert g.strand == "forward"
assert g.seq == "TTGGCAGATTCCCGCCAGAGCAAAACAGCCGCTAGTCCTAGTCCGAGTCGCCCGCAAAGTTCCTCGAATAACTCCGTACCCGGAGCGCCAAACCGGGTCTCCTTCGCTAAGCTGCGCGAACCACTTGAGGTTCCGGGACTCCTTGACGTCCAGACCGATTCGTTCGAGTGGCTGATCGGTTCGCCGCGCTGGCGCGAATCCGCCGCCGAGCGGGGTGATGTCAACCCAGTGGGTGGCCTGGAAGAGGTGCTCTACGAGCTGTCTCCGATCGAGGACTTCTCCGGGTCGATGTCGTTGTCGTTCTCTGACCCTCGTTTCGACGATGTCAAGGCACCCGTCGACGAGTGCAAAGACAAGGACATGACGTACGCGGCTCCACTGTTCGTCACCGCCGAGTTCATCAACAACAACACCGGTGAGATCAAGAGTCAGACGGTGTTCATGGGTGACTTCCCGATGATGACCGAGAAGGGCACGTTCATCATCAACGGGACCGAGCGTGTGGTGGTCAGCCAGCTGGTGCGGTCGCCCGGGGTGTACTTCGACGAGACCATTGACAAGTCCACCGACAAGACGCTGCACAGCGTCAAGGTGATCCCGAGCCGCGGCGCGTGGCTCGAGTTTGACGTCGACAAGCGCGACACCGTCGGCGTGCGCATCGACCGCAAACGCCGGCAACCGGTCACCGTGCTGCTCAAGGCGCTGGGCTGGACCAGCGAGCAGATTGTCGAGCGGTTCGGGTTCTCCGAGATCATGCGATCGACGCTGGAGAAGGACAACACCGTCGGCACCGACGAGGCGCTGTTGGACATCTACCGCAAGCTGCGTCCGGGCGAGCCCCCGACCAAAGAGTCAGCGCAGACGCTGTTGGAAAACTTGTTCTTCAAGGAGAAGCGCTACGACCTGGCCCGCGTCGGTCGCTATAAGGTCAACAAGAAGCTCGGGCTGCATGTCGGCGAGCCCATCACGTCGTCGACGCTGACCGAAGAAGACGTCGTGGCCACCATCGAATATCTGGTCCGCTTGCACGAGGGTCAGACCACGATGACCGTTCCGGGCGGCGTCGAGGTGCCGGTGGAAACCGACGACATCGACCACTTCGGCAACCGCCGCCTGCGTACGGTCGGCGAGCTGATCCAAAACCAGATCCGGGTCGGCATGTCGCGGATGGAGCGGGTGGTCCGGGAGCGGATGACCACCCAGGACGTGGAGGCGATCACACCGCAGACGTTGATCAACATCCGGCCGGTGGTCGCCGCGATCAAGGAGTTCTTCGGCACCAGCCAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTGGGGCCCGGCGGTCTGTCACGTGAGCGTGCCGGGCTGGAGGTCCGCGACGTGCACCCGTCGCACTACGGCCGGATGTGCCCGATCGAAACCCCTGAGGGGCCCAACATCGGTCTGATCGGCTCGCTGTCGGTGTACGCGCGGGTCAACCCGTTCGGGTTCATCGAAACGCCGTACCGCAAGGTGGTCGACGGCGTGGTTAGCGACGAGATCGTGTACCTGACCGCCGACGAGGAGGACCGCCACGTGGTGGCACAGGCCAATTCGCCGATCGATGCGGACGGTCGCTTCGTCGAGCCGCGCGTGCTGGTCCGCCGCAAGGCGGGCGAGGTGGAGTACGTGCCCTCGTCTGAGGTGGACTACATGGACGTCTCGCCCCGCCAGATGGTGTCGGTGGCCACCGCGATGATTCCCTTCCTGGAGCACGACGACGCCAACCGTGCCCTCATGGGGGCAAACATGCAGCGCCAGGCGGTGCCGCTGGTCCGTAGCGAGGCCCCGCTGGTGGGCACCGGGATGGAGCTGCGCGCGGCGATCGACGCCGGCGACGTCGTCGTCGCCGAAGAAAGCGGCGTCATCGAGGAGGTGTCGGCCGACTACATCACTGTGATGCACGACAACGGCACCCGGCGTACCTACCGGATGCGCAAGTTTGCCCGGTCCAACCACGGCACTTGCGCCAACCAGTGCCCCATCGTGGACGCGGGCGACCGAGTCGAGGCCGGTCAGGTGATCGCCGACGGTCCCTGTACTGACGACGGCGAGATGGCGCTGGGCAAGAACCTGCTGGTGGCCATCATGCCGTGGGAGGGCCACAACTACGAGGACGCGATCATCCTGTCCAACCGCCTGGTCGAAGAGGACGTGCTCACCTCGATCCACATCGAGGAGCATGAGATCGATGCTCGCGACACCAAGCTGGGTGCGGAGGAGATCACCCGCGACATCCCGAACATCTCCGACGAGGTGCTCGCCGACCTGGATGAGCGGGGCATCGTGCGCATCGGTGCCGAGGTTCGCGACGGGGACATCCTGGTCGGCAAGGTCACCCCGAAGGGTGAGACCGAGCTGACGCCGGAGGAGCGGCTGCTGCGTGCCATCTTCGGTGAGAAGGCCCGCGAGGTGCGCGACACTTCGCTGAAGGTGCCGCACGGCGAATCCGGCAAGGTGATCGGCATTCGGGTGTTTTCCCGCGAGGACGAGGACGAGTTGCCGGCCGGTGTCAACGAGCTGGTGCGTGTGTATGTGGCTCAGAAACGCAAGATCTCCGACGGTGACAAGCTGGCCGGCCGGCACGGCAACAAGGGCGTGATCGGCAAGATCCTGCCGGTTGAGGACATGCCGTTCCTTGCCGACGGCACCCCGGTGGACATTATTTTGAACACCCACGGCGTGCCGCGACGGATGAACATCGGCCAGATTTTGGAGACCCACCTGGGTTGGTGTGCCCACAGCGGCTGGAAGGTCGACGCCGCCAAGGGGGTTCCGGACTGGGCCGCCAGGCTGCCCGACGAACTGCTCGAGGCGCAGCCGAACGCCATTGTGTCGACGCCGGTGTTCGACGGCGCCCAGGAGGCCGAGCTGCAGGGCCTGTTGTCGTGCACGCTGCCCAACCGCGACGGTGACGTGCTGGTCGACGCCGACGGCAAGGCCATGCTCTTCGACGGGCGCAGCGGCGAGCCGTTCCCGTACCCGGTCACGGTTGGCTACATGTACATCATGAAGCTGCACCACCTGGTGGACGACAAGATCCACGCCCGCTCCACCGGGCCGTACTCGATGATCACCCAGCAGCCGCTGGGCGGTAAGGCGCAGTTCGGTGGCCAGCGGTTCGGGGAGATGGAGTGCTGGGCCATGCAGGCCTACGGTGCTGCCTACACCCTGCAGGAGCTGTTGACCATCAAGTCCGATGACACCGTCGGCCGCGTCAAGGTGTACGAGGCGATCGTCAAGGGTGAGAACATCCCGGAGCCGGGCATCCCCGAGTCGTTCAAGGTGCTGCTCAAAGAACTGCAGTCGCTGTGCCTCAACGTCGAGGTGCTATCGAGTGACGGTGCGGCGATCGAACTGCGCGAAGGTGAGGACGAGGACCTGGAGCGGGCCGCGGCCAACCTGGGAATCAATCTGTCCCGCAACGAATCCGCAAGTGTCGAGGATCTTGCGTAA"
assert g.prot == "LADSRQSKTAASPSPSRPQSSSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEAQPNAIVSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASVEDLA"
DB.drop_database('mykrobe-test')
def test_reverse_gene(self):
g = Gene(name="gidB",
reference=self.reference_seq,
start=4407528,
end=4408202,
forward=False)
assert g.name == "gidB"
assert g.forward is False
assert g.strand == "reverse"
assert g.seq == "ATGTCTCCGATCGAGCCCGCGGCGTCTGCGATCTTCGGACCGCGGCTTGGCCTTGCTCGGCGGTACGCCGAAGCGTTGGCGGGACCCGGTGTGGAGCGGGGGCTGGTGGGACCCCGCGAAGTCGGTAGGCTATGGGACCGGCATCTACTGAACTGCGCCGTGATCGGTGAGCTCCTCGAACGCGGTGACCGGGTCGTGGATATCGGTAGCGGAGCCGGGTTGCCGGGCGTGCCATTGGCGATAGCGCGGCCGGACCTCCAGGTAGTTCTCCTAGAACCGCTACTGCGCCGCACCGAGTTTCTTCGAGAGATGGTGACAGATCTGGGCGTGGCCGTTGAGATCGTGCGGGGGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAGCATGCCGTTGATACGGCCGAACGGGCGAATGCTCGCCATCAAAGGCGAGCGGGCTCACGACGAAGTACGGGAGCACCGGCGTGTGATGATCGCATCGGGCGCGGTTGATGTCAGGGTGGTGACATGTGGCGCGAACTATTTGCGTCCGCCCGCGACCGTGGTGTTCGCACGACGTGGAAAGCAGATCGCCCGAGGGTCGGCACGGATGGCGAGTGGAGGGACGGCGTGA"
assert g.prot == "MSPIEPAASAIFGPRLGLARRYAEALAGPGVERGLVGPREVGRLWDRHLLNCAVIGELLERGDRVVDIGSGAGLPGVPLAIARPDLQVVLLEPLLRRTEFLREMVTDLGVAVEIVRGRAEESWVQDQLGGSDAAVSRAVAALDKLTKWSMPLIRPNGRMLAIKGERAHDEVREHRRVMIASGAVDVRVVTCGANYLRPPATVVFARRGKQIARGSARMASGGTA"
DB.drop_database('mykrobe-test')
def test_reverse_gene2(self):
g = Gene(name="katG",
reference=self.reference_seq,
start=2153889,
end=2156111,
forward=False)
assert g.name == "katG"
assert g.forward is False
assert g.strand == "reverse"
assert g.seq == "GTGCCCGAGCAACACCCACCCATTACAGAAACCACCACCGGAGCCGCTAGCAACGGCTGTCCCGTCGTGGGTCATATGAAATACCCCGTCGAGGGCGGCGGAAACCAGGACTGGTGGCCCAACCGGCTCAATCTGAAGGTACTGCACCAAAACCCGGCCGTCGCTGACCCGATGGGTGCGGCGTTCGACTATGCCGCGGAGGTCGCGACCATCGACGTTGACGCCCTGACGCGGGACATCGAGGAAGTGATGACCACCTCGCAGCCGTGGTGGCCCGCCGACTACGGCCACTACGGGCCGCTGTTTATCCGGATGGCGTGGCACGCTGCCGGCACCTACCGCATCCACGACGGCCGCGGCGGCGCCGGGGGCGGCATGCAGCGGTTCGCGCCGCTTAACAGCTGGCCCGACAACGCCAGCTTGGACAAGGCGCGCCGGCTGCTGTGGCCGGTCAAGAAGAAGTACGGCAAGAAGCTCTCATGGGCGGACCTGATTGTTTTCGCCGGCAACTGCGCGCTGGAATCGATGGGCTTCAAGACGTTCGGGTTCGGCTTCGGCCGGGTCGACCAGTGGGAGCCCGATGAGGTCTATTGGGGCAAGGAAGCCACCTGGCTCGGCGATGAGCGTTACAGCGGTAAGCGGGATCTGGAGAACCCGCTGGCCGCGGTGCAGATGGGGCTGATCTACGTGAACCCGGAGGGGCCGAACGGCAACCCGGACCCCATGGCCGCGGCGGTCGACATTCGCGAGACGTTTCGGCGCATGGCCATGAACGACGTCGAAACAGCGGCGCTGATCGTCGGCGGTCACACTTTCGGTAAGACCCATGGCGCCGGCCCGGCCGATCTGGTCGGCCCCGAACCCGAGGCTGCTCCGCTGGAGCAGATGGGCTTGGGCTGGAAGAGCTCGTATGGCACCGGAACCGGTAAGGACGCGATCACCAGCGGCATCGAGGTCGTATGGACGAACACCCCGACGAAATGGGACAACAGTTTCCTCGAGATCCTGTACGGCTACGAGTGGGAGCTGACGAAGAGCCCTGCTGGCGCTTGGCAATACACCGCCAAGGACGGCGCCGGTGCCGGCACCATCCCGGACCCGTTCGGCGGGCCAGGGCGCTCCCCGACGATGCTGGCCACTGACCTCTCGCTGCGGGTGGATCCGATCTATGAGCGGATCACGCGTCGCTGGCTGGAACACCCCGAGGAATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGCTGATCCACCGAGACATGGGTCCCGTTGCGAGATACCTTGGGCCGCTGGTCCCCAAGCAGACCCTGCTGTGGCAGGATCCGGTCCCTGCGGTCAGCCACGACCTCGTCGGCGAAGCCGAGATTGCCAGCCTTAAGAGCCAGATCCGGGCATCGGGATTGACTGTCTCACAGCTAGTTTCGACCGCATGGGCGGCGGCGTCGTCGTTCCGTGGTAGCGACAAGCGCGGCGGCGCCAACGGTGGTCGCATCCGCCTGCAGCCACAAGTCGGGTGGGAGGTCAACGACCCCGACGGGGATCTGCGCAAGGTCATTCGCACCCTGGAAGAGATCCAGGAGTCATTCAACTCCGCGGCGCCGGGGAACATCAAAGTGTCCTTCGCCGACCTCGTCGTGCTCGGTGGCTGTGCCGCCATAGAGAAAGCAGCAAAGGCGGCTGGCCACAACATCACGGTGCCCTTCACCCCGGGCCGCACGGATGCGTCGCAGGAACAAACCGACGTGGAATCCTTTGCCGTGCTGGAGCCCAAGGCAGATGGCTTCCGAAACTACCTCGGAAAGGGCAACCCGTTGCCGGCCGAGTACATGCTGCTCGACAAGGCGAACCTGCTTACGCTCAGTGCCCCTGAGATGACGGTGCTGGTAGGTGGCCTGCGCGTCCTCGGCGCAAACTACAAGCGCTTACCGCTGGGCGTGTTCACCGAGGCCTCCGAGTCACTGACCAACGACTTCTTCGTGAACCTGCTCGACATGGGTATCACCTGGGAGCCCTCGCCAGCAGATGACGGGACCTACCAGGGCAAGGATGGCAGTGGCAAGGTGAAGTGGACCGGCAGCCGCGTGGACCTGGTCTTCGGGTCCAACTCGGAGTTGCGGGCGCTTGTCGAGGTCTATGGCGCCGATGACGCGCAGCCGAAGTTCGTGCAGGACTTCGTCGCTGCCTGGGACAAGGTGATGAACCTCGACAGGTTCGACGTGCGCTGA"
assert g.prot == "VPEQHPPITETTTGAASNGCPVVGHMKYPVEGGGNQDWWPNRLNLKVLHQNPAVADPMGAAFDYAAEVATIDVDALTRDIEEVMTTSQPWWPADYGHYGPLFIRMAWHAAGTYRIHDGRGGAGGGMQRFAPLNSWPDNASLDKARRLLWPVKKKYGKKLSWADLIVFAGNCALESMGFKTFGFGFGRVDQWEPDEVYWGKEATWLGDERYSGKRDLENPLAAVQMGLIYVNPEGPNGNPDPMAAAVDIRETFRRMAMNDVETAALIVGGHTFGKTHGAGPADLVGPEPEAAPLEQMGLGWKSSYGTGTGKDAITSGIEVVWTNTPTKWDNSFLEILYGYEWELTKSPAGAWQYTAKDGAGAGTIPDPFGGPGRSPTMLATDLSLRVDPIYERITRRWLEHPEELADEFAKAWYKLIHRDMGPVARYLGPLVPKQTLLWQDPVPAVSHDLVGEAEIASLKSQIRASGLTVSQLVSTAWAAASSFRGSDKRGGANGGRIRLQPQVGWEVNDPDGDLRKVIRTLEEIQESFNSAAPGNIKVSFADLVVLGGCAAIEKAAKAAGHNITVPFTPGRTDASQEQTDVESFAVLEPKADGFRNYLGKGNPLPAEYMLLDKANLLTLSAPEMTVLVGGLRVLGANYKRLPLGVFTEASESLTNDFFVNLLDMGITWEPSPADDGTYQGKDGSGKVKWTGSRVDLVFGSNSELRALVEVYGADDAQPKFVQDFVAAWDKVMNLDRFDVR"
DB.drop_database('mykrobe-test')
def test_get_codon(self):
g = Gene(name="rpoB",
reference=self.reference_seq,
start=759807,
end=763325)
with pytest.raises(ValueError):
g.get_codon(1173)
assert g.get_codon(2) == "GCA"
assert g.get_codon(3) == "GAT"
assert g.get_reference_position(1) == 759807
assert g.seq[0] == self.reference_seq[759806]
assert g.get_reference_position(-1) == 759806
DB.drop_database('mykrobe-test')
def test_get_codon_reverse(self):
g = Gene(name="gidB",
reference=self.reference_seq,
start=4407528,
end=4408202,
forward=False)
with pytest.raises(ValueError):
g.get_codon(225)
assert g.get_codon(2) == "TCT"
assert g.get_codon(3) == "CCG"
assert g.get_reference_position(1) == 4408202
assert g.get_reference_position(2) == 4408201
assert g.get_reference_position(-1) == 4408203
assert g.get_reference_position(-2) == 4408204
DB.drop_database('mykrobe-test')
def test_gene_muts(self):
self.gm = GeneAminoAcidChangeToDNAVariants(
reference="src/mykrobe/data/NC_000962.3.fasta",
genbank="src/mykrobe/data/NC_000962.3.gb")
assert self.gm.get_alts("K") == ['AAA', 'AAG']
# GAT -> ['GCA', 'GCT', 'GCC', 'GCG'], positions 759813,14,15
assert sorted(self.gm.get_variant_names("rpoB", "D3A")) == sorted(
['GAT759813GCA', 'GAT759813GCT', 'GAT759813GCC', 'GAT759813GCG'])
# GAT -> ['GCA', 'GCT', 'GCC', 'GCG'], positions 759813,14,15
assert sorted(self.gm.get_variant_names("rpoB", "D3X")) == sorted([
'GAT759813GCA', 'GAT759813GCT', 'GAT759813GCC', 'GAT759813GCG',
'GAT759813TGT', 'GAT759813TGC', 'GAT759813GAA', 'GAT759813GAG',
'GAT759813GGA', 'GAT759813GGT', 'GAT759813GGC', 'GAT759813GGG',
'GAT759813TTT', 'GAT759813TTC', 'GAT759813ATA', 'GAT759813ATT',
'GAT759813ATC', 'GAT759813CAT', 'GAT759813CAC', 'GAT759813AAA',
'GAT759813AAG', 'GAT759813ATG', 'GAT759813TTA', 'GAT759813TTG',
'GAT759813CTA', 'GAT759813CTT', 'GAT759813CTC', 'GAT759813CTG',
'GAT759813AAT', 'GAT759813AAC', 'GAT759813CAA', 'GAT759813CAG',
'GAT759813CCA', 'GAT759813CCT', 'GAT759813CCC', 'GAT759813CCG',
'GAT759813AGT', 'GAT759813AGC', 'GAT759813TCA', 'GAT759813TCT',
'GAT759813TCC', 'GAT759813TCG', 'GAT759813AGA', 'GAT759813AGG',
'GAT759813CGA', 'GAT759813CGT', 'GAT759813CGC', 'GAT759813CGG',
'GAT759813ACA', 'GAT759813ACT', 'GAT759813ACC', 'GAT759813ACG',
'GAT759813TGG', 'GAT759813GTA', 'GAT759813GTT', 'GAT759813GTC',
'GAT759813GTG', 'GAT759813TAT', 'GAT759813TAC'
])
DB.drop_database('mykrobe-test')
def test_gene_muts2(self):
self.gm = GeneAminoAcidChangeToDNAVariants(
reference="src/mykrobe/data/NC_000962.3.fasta",
genbank="src/mykrobe/data/NC_000962.3.gb")
assert self.gm.get_alts("K") == ['AAA', 'AAG']
# AGC -> ['CTT', 'CTC', 'CTA', 'CTG']
# # GAG -> ['GCA', 'GCT', 'GCC', 'GCG']
# RC : CTC -> ['TGC',...] position2156103
assert sorted(self.gm.get_variant_names("katG", "E3A")) == sorted([
'CTC2156103TGC', 'CTC2156103AGC', 'CTC2156103GGC', 'CTC2156103CGC'
])
DB.drop_database('mykrobe-test')
def test_make_variant_panel1(self):
ag = AlleleGenerator("src/mykrobe/data/NC_000962.3.fasta")
gene = self.gm.get_gene("rpoB")
for var in self.gm.get_variant_names("rpoB", "D3A"):
ref, start, alt = split_var_name(var)
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference_id,
reference_bases=ref,
start=start,
alternate_bases=[alt])
panel = ag.create(v)
for alt in panel.alts:
seq = copy.copy(str(gene.seq))
assert Seq(seq).translate()[2] == "D"
seq = seq.replace(panel.refs[0][25:], alt[24:])
assert seq != str(gene.seq)
assert Seq(seq).translate()[2] == "A"
DB.drop_database('mykrobe-test')
def test_make_variant_panel2(self):
ag = AlleleGenerator("src/mykrobe/data/NC_000962.3.fasta")
gene = self.gm.get_gene("katG")
for var in self.gm.get_variant_names("katG", "E3A"):
ref, start, alt = split_var_name(var)
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference_id,
reference_bases=ref,
start=start,
alternate_bases=[alt])
panel = ag.create(v)
for alt in panel.alts:
seq = copy.copy(str(gene.seq.reverse_complement()))
seq = seq.replace(panel.refs[0][:39],
alt[:39 + len(alt) - len(panel.refs[0])])
assert seq != str(gene.seq)
assert Seq(seq).reverse_complement().translate()[2] == "A"
DB.drop_database('mykrobe-test')
def test_make_variant_panel3(self):
ag = AlleleGenerator("src/mykrobe/data/NC_000962.3.fasta")
gene = self.gm.get_gene("katG")
for var in self.gm.get_variant_names("katG", "S315L"):
ref, start, alt = split_var_name(var)
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference_id,
reference_bases=ref,
start=start,
alternate_bases=[alt])
panel = ag.create(v)
for alt in panel.alts:
seq = copy.copy(str(gene.seq.reverse_complement()))
seq = seq.replace(panel.refs[0], alt)
assert seq != str(gene.seq)
assert Seq(seq).reverse_complement().translate()[314] == "L"
DB.drop_database('mykrobe-test')
def test_make_variant_panel4(self):
ag = AlleleGenerator("src/mykrobe/data/NC_000962.3.fasta")
gene = self.gm.get_gene("katG")
for var in self.gm.get_variant_names("katG", "W90R"):
ref, start, alt = split_var_name(var)
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference_id,
reference_bases=ref,
start=start,
alternate_bases=[alt])
panel = ag.create(v)
for alt in panel.alts:
seq = copy.copy(str(gene.seq.reverse_complement()))
seq = seq.replace(panel.refs[0], alt)
assert seq != str(gene.seq)
assert Seq(seq).reverse_complement().translate()[89] == "R"
DB.drop_database('mykrobe-test')
def test_make_variant_panel5(self):
ag = AlleleGenerator("src/mykrobe/data/NC_000962.3.fasta")
gene = self.gm.get_gene("gyrA")
for var in self.gm.get_variant_names("gyrA", "D94X"):
ref, start, alt = split_var_name(var)
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference_id,
reference_bases=ref,
start=start,
alternate_bases=[alt])
panel = ag.create(v)
for alt in panel.alts:
seq = copy.copy(str(gene.seq))
seq = seq.replace(panel.refs[0], alt)
assert Seq(seq).translate()[93] != "D"
DB.drop_database('mykrobe-test')
def test_make_variant_panel6(self):
ag = AlleleGenerator("src/mykrobe/data/NC_000962.3.fasta")
gene = self.gm.get_gene("pncA")
variants = list(
self.gm.get_variant_names("pncA",
"CAG28TAA",
protein_coding_var=False))
assert len(variants) == 1
var = variants[0]
ref, start, alt = split_var_name(var)
assert ref == 'CTG'
assert start == 2289212
assert alt == 'TTA'
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference_id,
reference_bases=ref,
start=start,
alternate_bases=[alt])
panel = ag.create(v)
assert len(panel.alts) == 1
alt = panel.alts[0]
# the panel ref/alt seqs go past the end of the gene,
# so can't comparie against gene sequence. Need to get
# subseq from the reference seq
panel_ref_start = self.reference_seq.find(panel.refs[0])
assert panel_ref_start < start < panel_ref_start + len(panel.refs[0])
seq = str(self.reference_seq[panel_ref_start:panel_ref_start +
len(panel.refs[0])])
assert seq == panel.refs[0]
assert alt == seq[:30] + 'TTA' + seq[33:]
DB.drop_database('mykrobe-test')
def test_make_variant_panel7(self):
# Test DNA change upstream of a gene on the reverse
# strand. The variant G-10A is in "gene space", ie
# 10 bases upstream of eis is the nucleotide G on the
# reverse strand. That position is 2715342 in the genome,
# and is C on the forwards strand.
# Here's a diagram:
# | <- This C is at -10 in "gene space", so variant G-10A has ref=G
# | ref coord is 2715342, and variant in "ref space" is C2715342T
# CACAGAATCCGACTGTGGCATATGCCGC
# |
# | <- C = last nucleotide of gene, at 2715332
ag = AlleleGenerator("src/mykrobe/data/NC_000962.3.fasta")
gene = self.gm.get_gene("eis")
variants = list(
self.gm.get_variant_names("eis", "G-10A",
protein_coding_var=False))
assert len(variants) == 1
var = variants[0]
ref, start, alt = split_var_name(var)
assert ref == 'C'
assert start == 2715342
assert alt == 'T'
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference_id,
reference_bases=ref,
start=start,
alternate_bases=[alt])
panel = ag.create(v)
assert len(panel.alts) == 1
alt = panel.alts[0]
# the panel ref/alt seqs go past the end of the gene,
# so can't comparie against gene sequence. Need to get
# subseq from the reference seq
panel_ref_start = self.reference_seq.find(panel.refs[0])
assert panel_ref_start < start < panel_ref_start + len(panel.refs[0])
seq = str(self.reference_seq[panel_ref_start:panel_ref_start +
len(panel.refs[0])])
assert seq == panel.refs[0]
assert alt == seq[:30] + 'T' + seq[31:]
DB.drop_database('mykrobe-test')
def test_make_variant_panel8(self):
ag = AlleleGenerator("src/mykrobe/data/NC_000962.3.fasta")
gene = self.gm.get_gene("eis")
variants = list(
self.gm.get_variant_names("eis", "TG-1T",
protein_coding_var=False))
assert len(variants) == 1
var = variants[0]
ref, start, alt = split_var_name(var)
assert ref == 'CA'
assert start == 2715332
assert alt == 'A'
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference_id,
reference_bases=ref,
start=start,
alternate_bases=[alt])
panel = ag.create(v)
assert len(panel.alts) == 1
alt = panel.alts[0]
# the panel ref/alt seqs go past the end of the gene,
# so can't comparie against gene sequence. Need to get
# subseq from the reference seq
panel_ref_start = self.reference_seq.find(panel.refs[0])
assert panel_ref_start < start < panel_ref_start + len(panel.refs[0])
seq = str(self.reference_seq[panel_ref_start:panel_ref_start +
len(panel.refs[0])])
assert seq == panel.refs[0]
print(alt, seq[:31] + seq[31:])
assert alt == seq[:30] + seq[31:]
DB.drop_database('mykrobe-test')
def run(parser, args):
DB = connect('mykrobe-%s' % (args.db_name))
if DB is not None:
try:
Variant.objects()
logging.info(
"Connected to mykrobe-%s" % (args.db_name))
except (ServerSelectionTimeoutError):
DB = None
logging.warning(
"Could not connect to database. Continuing without using genetic backgrounds")
mutations = []
reference = os.path.basename(args.reference_filepath).split('.fa')[0]
if args.vcf:
run_make_probes_from_vcf_file(args)
elif args.genbank:
aa2dna = GeneAminoAcidChangeToDNAVariants(
args.reference_filepath,
args.genbank)
if args.text_file:
with open(args.text_file, 'r') as infile:
reader = csv.reader(infile, delimiter="\t")
for row in reader:
gene, mutation_string, alphabet = row
if alphabet == "DNA":
protein_coding_var = False
else:
protein_coding_var = True
for var_name in aa2dna.get_variant_names(
gene, mutation_string, protein_coding_var):
mutation = Mutation(reference=reference,
var_name=var_name,
gene=aa2dna.get_gene(gene),
mut=mutation_string)
mutations.append(mutation)
else:
for variant in args.variants:
gene, mutation = variant.split("_")
for var_name in aa2dna.get_variant_names(gene, mutation):
mutations.append(
Mutation(reference=reference,
var_name=var_name,
gene=gene,
mut=mutation))
else:
if args.text_file:
with open(args.text_file, 'r') as infile:
reader = csv.reader(infile, delimiter="\t")
for row in reader:
gene_name, pos, ref, alt, alphabet = row
if gene_name == "ref":
mutations.append(
Mutation(
reference=reference,
var_name="".join([ref, pos, alt])))
else:
mutations.append(
Mutation(
reference=reference,
var_name=row[0]))
else:
mutations.extend(Mutation(reference=reference, var_name=v)
for v in args.variants)
al = AlleleGenerator(
reference_filepath=args.reference_filepath,
kmer=args.kmer)
for enum, mut in enumerate(mutations):
if enum % 100 == 0:
logger.info(
"%i of %i - %f%%" % (enum, len(mutations), round(100*enum/len(mutations), 2)))
variant_panel = make_variant_probe(
al, mut.variant, args.kmer, DB=DB, no_backgrounds=args.no_backgrounds)
if variant_panel is not None:
for i, ref in enumerate(variant_panel.refs):
try:
gene_name = mut.gene.name
except AttributeError:
gene_name = "NA"
sys.stdout.write(
">ref-%s?var_name=%s&num_alts=%i&ref=%s&enum=%i&gene=%s&mut=%s\n" %
(mut.mut, mut.variant.var_name, len(
variant_panel.alts), mut.reference, i, gene_name, mut.mut))
sys.stdout.write("%s\n" % ref)
for i, a in enumerate(variant_panel.alts):
sys.stdout.write(">alt-%s?var_name=%s&enum=%i&gene=%s&mut=%s\n" %
(mut.mut, mut.variant.var_name, i, gene_name, mut.mut))
sys.stdout.write("%s\n" % a)
else:
logging.warning(
"All variants failed for %s_%s - %s" %
(mut.gene, mut.mut, mut.variant))
def run(parser, args):
# There's no need to try to connect to database if we're not doing backgrounds
if args.no_backgrounds:
logger.info(
"Not connecting to database, because --no-backgrounds option used")
DB = None
else:
DB = connect("%s-%s" % (DB_PREFIX, args.db_name))
if DB is not None:
try:
Variant.objects()
logger.info("Connected to %s-%s" % (DB_PREFIX, args.db_name))
except (ServerSelectionTimeoutError):
DB = None
logger.warning(
"Could not connect to database. Continuing without using genetic backgrounds"
)
mutations = []
lineages = set()
reference = os.path.basename(args.reference_filepath).split(".fa")[0]
if args.vcf:
run_make_probes_from_vcf_file(args)
elif args.genbank:
aa2dna = GeneAminoAcidChangeToDNAVariants(args.reference_filepath,
args.genbank)
if args.text_file:
with open(args.text_file, "r") as infile:
reader = csv.reader(infile, delimiter="\t")
for row in reader:
gene, mutation_string, alphabet = row
if alphabet == "DNA":
protein_coding_var = False
else:
protein_coding_var = True
for var_name in aa2dna.get_variant_names(
gene, mutation_string, protein_coding_var):
mutation = Mutation(
reference=reference,
var_name=var_name,
gene=aa2dna.get_gene(gene),
mut=mutation_string,
protein_coding_var=protein_coding_var,
)
mutations.append(mutation)
else:
for variant in args.variants:
gene, mutation = variant.split("_")
for var_name in aa2dna.get_variant_names(gene, mutation):
mutations.append(
Mutation(
reference=reference,
var_name=var_name,
gene=gene,
mut=mutation,
))
else:
if args.text_file:
mutations, lineages = load_dna_vars_txt_file(
args.text_file, reference)
if args.lineage:
with open(args.lineage, "w") as f:
json.dump(lineages, f, sort_keys=True, indent=2)
else:
mutations.extend(
Mutation(reference=reference, var_name=v)
for v in args.variants)
al = AlleleGenerator(reference_filepath=args.reference_filepath,
kmer=args.kmer)
for enum, mut in enumerate(mutations):
if enum % 100 == 0:
logger.info(
"%i of %i - %f%%" %
(enum, len(mutations), round(100 * enum / len(mutations), 2)))
variant_panel = make_variant_probe(al,
mut.variant,
args.kmer,
DB=DB,
no_backgrounds=args.no_backgrounds)
if variant_panel is not None:
for i, ref in enumerate(variant_panel.refs):
try:
gene_name = mut.gene.name
except AttributeError:
gene_name = "NA"
sys.stdout.write(
">ref-%s?var_name=%s&num_alts=%i&ref=%s&enum=%i&gene=%s&mut=%s\n"
% (
mut.mutation_output_name,
mut.variant.var_name,
len(variant_panel.alts),
mut.reference,
i,
gene_name,
mut.mutation_output_name,
))
sys.stdout.write("%s\n" % ref)
for i, a in enumerate(variant_panel.alts):
sys.stdout.write(
">alt-%s?var_name=%s&enum=%i&gene=%s&mut=%s\n" % (
mut.mutation_output_name,
mut.variant.var_name,
i,
gene_name,
mut.mutation_output_name,
))
sys.stdout.write("%s\n" % a)
else:
logger.warning("All variants failed for %s_%s - %s" %
(mut.gene, mut.mutation_output_name, mut.variant))