def test_parse_legacy_blasttab(anib_output):
"""Parses ANIB legacy .blast_tab output."""
fragdata = anib.get_fraglength_dict([anib_output.fragfile])
result = anib.parse_blast_tab(anib_output.legacytabfile,
fragdata,
mode="ANIblastall")
assert (
a == b
for a, b in zip(result, [1_966_922, 406_104, 78.578_978_313_253_018]))
def test_parse_blastdir(anib_output_dir):
"""Parse directory of BLAST+ output."""
orglengths = pyani_files.get_sequence_lengths(anib_output_dir.infiles)
fraglengths = anib.get_fraglength_dict(anib_output_dir.fragfiles)
result = anib.process_blast(anib_output_dir.blastdir,
orglengths,
fraglengths,
mode="ANIb")
assert_frame_equal(
result.percentage_identity.sort_index(1).sort_index(),
anib_output_dir.blastresult.sort_index(1).sort_index(),
)
def test_legacy_blastdir_processing(self):
"""parse directory of legacy .blast_tab output"""
orglengths = pyani_files.get_sequence_lengths(self.infnames)
fraglengths = anib.get_fraglength_dict(self.fragfiles)
# ANIblastall
result = anib.process_blast(self.aniblastalldir,
orglengths,
fraglengths,
mode="ANIblastall")
assert_frame_equal(
result.percentage_identity.sort_index(1).sort_index(),
self.aniblastalltgt.sort_index(1).sort_index(),
)
def test_parse_blasttab(self):
"""parses ANIblastall .blast_tab output."""
fragdata = anib.get_fraglength_dict([self.fragfname])
# ANIb output
result = anib.parse_blast_tab(self.fname,
fragdata,
0.3,
0.7,
mode="ANIb")
assert_equal(result, (4016551, 93, 99.997693577050029))
# ANIblastall output
result = anib.parse_blast_tab(self.fname_legacy,
fragdata,
0.3,
0.7,
mode="ANIblastall")
assert_equal(result, (1966922, 406104, 78.578978313253018))
def test_parse_blasttab(anib_output):
"""Parse ANIb BLAST+ .blast_tab output."""
fragdata = anib.get_fraglength_dict([anib_output.fragfile])
result = anib.parse_blast_tab(anib_output.tabfile, fragdata, mode="ANIb")
assert (a == b
for a, b in zip(result, [4_016_551, 93, 99.997_693_577_050_029]))