def test_tab_2228_tblastx_001(self):
"Test parsing TBLASTX 2.2.28+ tabular output (tab_2228_tblastx_001)"
tab_file = get_file('tab_2228_tblastx_001.txt')
qresults = list(parse(tab_file, FMT,
fields=list(all_fields.values()),
comments=True))
# this a single query, with 192 hits and 243 hsps
self.assertEqual(1, len(qresults))
self.assertEqual(192, len(qresults[0].hits))
self.assertEqual(243, sum([len(x) for x in qresults[0]]))
# only checking the new fields in 2.2.28+
hit = qresults[0][0]
self.assertEqual(['NM_001183135', 'EF059095'], hit.accession_all)
self.assertEqual(['32630', '559292'], hit.tax_ids)
self.assertEqual(['N/A', 'N/A'], hit.sci_names)
self.assertEqual(['N/A', 'N/A'], hit.com_names)
self.assertEqual(['N/A'], hit.blast_names)
self.assertEqual(['N/A'], hit.super_kingdoms)
self.assertEqual('Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA', hit.title)
self.assertEqual(['Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA',
'Synthetic construct Saccharomyces cerevisiae clone '
'FLH203015.01X MON2, complete sequence'], hit.title_all)
self.assertEqual('N/A', hit.strand)
self.assertEqual(100.0, hit.query_coverage)
for hsp in hit[:4]:
# shorthand ~ the values just happen to all be 99
# in other cases, they may be different
self.assertEqual(99.0, hsp.query_coverage)
self.assertEqual(73.0, hit[5].query_coverage)
self.assertEqual(12.0, hit[6].query_coverage)
def test_tab_2228_tblastx_001(self):
"""Test parsing TBLASTX 2.2.28+ tabular output (tab_2228_tblastx_001)."""
tab_file = get_file("tab_2228_tblastx_001.txt")
qresults = list(
parse(tab_file,
FMT,
fields=list(all_fields.values()),
comments=True))
# this a single query, with 192 hits and 243 hsps
self.assertEqual(1, len(qresults))
self.assertEqual(192, len(qresults[0].hits))
self.assertEqual(243, sum(len(x) for x in qresults[0]))
# there is one hit with an alternative ID
self.assertEqual(
qresults[0]["gi|31126987|gb|AY255526.2|"],
qresults[0]["gi|31342050|ref|NM_181083.2|"],
)
# only checking the new fields in 2.2.28+
hit = qresults[0][0]
self.assertEqual(["NM_001183135", "EF059095"], hit.accession_all)
self.assertEqual(["32630", "559292"], hit.tax_ids)
self.assertEqual(["N/A", "N/A"], hit.sci_names)
self.assertEqual(["N/A", "N/A"], hit.com_names)
self.assertEqual(["N/A"], hit.blast_names)
self.assertEqual(["N/A"], hit.super_kingdoms)
self.assertEqual("Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA",
hit.title)
self.assertEqual(
[
"Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA",
"Synthetic construct Saccharomyces cerevisiae clone "
"FLH203015.01X MON2, complete sequence",
],
hit.title_all,
)
self.assertEqual("N/A", hit.strand)
self.assertEqual(100.0, hit.query_coverage)
for hsp in hit[:4]:
# shorthand ~ the values just happen to all be 99
# in other cases, they may be different
self.assertEqual(99.0, hsp.query_coverage)
self.assertEqual(73.0, hit[5].query_coverage)
self.assertEqual(12.0, hit[6].query_coverage)