def test_duplicatePosition_raisesError(self):
stream = StringIO(
"lineage1,615938,1104,G/A,368,GAG/GAA,E/E,Rv0524,hemL\n"
"lineage1,615938,1104,G/A,368,GAG/GAA,E/E,Rv0524,hemL\n"
)
with pytest.raises(IndexError):
load_panel(stream)
def test_headerOnly_returnsEmpty(self):
stream = StringIO("header,line\n")
actual = load_panel(stream, no_header=False)
expected = dict()
assert actual == expected
def test_emptyFile_returnsEmpty(self):
stream = StringIO()
actual = load_panel(stream)
expected = dict()
assert actual == expected
def test_noHeader_allPanelVariantsInPanel(self):
stream = StringIO(
"lineage1,615938,1104,G/A,368,GAG/GAA,E/E,Rv0524,hemL\n"
"lineage1.1,4404247,1056,G/A,352,CTG/CTA,L/L,Rv3915,-"
)
actual = load_panel(stream)
expected = {
615938: PanelVariant(
Lineage("1"), 615938, "G", "A", "Rv0524", "hemL", 1104
),
4404247: PanelVariant(
Lineage("1", "1"), 4404247, "G", "A", "Rv3915", "-", 1056
),
}
assert actual == expected
def test_fileWithNoIssues_loadsOk(self):
stream = StringIO(
"lineage,position,gene_coord,allele_change,codon_number,codon_change,amino_acid_change,locus_id,gene_name\n"
"lineage1,615938,1104,G/A,368,GAG/GAA,E/E,Rv0524,hemL\n"
"lineage1.1,4404247,1056,G/A,352,CTG/CTA,L/L,Rv3915,-"
)
actual = load_panel(stream, no_header=False)
expected = {
615938: PanelVariant(
Lineage("1"), 615938, "G", "A", "Rv0524", "hemL", 1104
),
4404247: PanelVariant(
Lineage("1", "1"), 4404247, "G", "A", "Rv3915", "-", 1056
),
}
assert actual == expected
def test_nonDefaultDelim_loadsOk(self):
stream = StringIO(
"lineage1|615938|1104|G/A|368|GAG/GAA|E/E|Rv0524|hemL\n"
"lineage1.1|4404247|1056|G/A|352|CTG/CTA|L/L|Rv3915|-"
)
delim = "|"
actual = load_panel(stream, delim=delim)
expected = {
615938: PanelVariant(
Lineage("1"), 615938, "G", "A", "Rv0524", "hemL", 1104
),
4404247: PanelVariant(
Lineage("1", "1"), 4404247, "G", "A", "Rv3915", "-", 1056
),
}
assert actual == expected