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Fix ambig typos

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This commit is contained in:
Peter Cock
2021-08-30 12:22:25 +01:00
parent 7dc62f2df4
commit 7b0c62ed39
6 changed files with 15 additions and 16 deletions
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9
Tests/Ace/contig1.ace
View File

@ -595,7 +595,7 @@ BL060c3-LR5.g.ab1 matchElsewhereHighQual phrap 617 631 040217:110357
}
CT{
Contig2 repeat phrap 42 43 123456:765432
This is the forst line of comment for c2
This is the first line of comment for c2
and this the second for c2
}
RD BL060-LR8.5.g.ab1 877 0 0
@ -841,20 +841,19 @@ BL060c5-LR0R.b.ab1 matchElsewhereHighQual phrap 617 631 040217:110357
CT{
unrelated_Contig repeat phrap 1142 143 122226:722232
This is the forst line of comment for the unrelated ct tag
This is the first line of comment for the unrelated ct tag
and this the second
}
CT{
Contig1 repeat phrap 52 53 555456:555432
This is the forst line of comment for c1
This is the first line of comment for c1
and this the second for c1
}
WA{
phrap_params phrap 040203:114710
phrap 304_nuclsu.fasta.screen -new_ace -retain_duplicates
phrap 304_nuclsu.fasta.screen -new_ace -retain_duplicates
phrap version 0.990329
}

2
Tests/common_BioSQL_online.py
View File

@ -122,7 +122,7 @@ class TaxonomyTest(unittest.TestCase):
test_record = self.db.lookup(accession="X55053")
# make sure that the ncbi taxonomy id is corrent
# make sure that the ncbi taxonomy id is correct
self.assertEqual(test_record.annotations["ncbi_taxid"], 3702)
# make sure that the taxonomic lineage is the same as reported
# using the Entrez module

10
Tests/test_Ace.py
View File

@ -79,7 +79,7 @@ class AceTestOne(unittest.TestCase):
self.assertEqual(record.contigs[0].ct[0].date, "555456:555432")
self.assertEqual(
record.contigs[0].ct[0].info,
["This is the forst line of comment for c1", "and this the second for c1"],
["This is the first line of comment for c1", "and this the second for c1"],
)
self.assertIsNone(record.contigs[0].wa)
self.assertEqual(len(record.contigs[0].reads), 2)
@ -201,7 +201,7 @@ class AceTestOne(unittest.TestCase):
self.assertEqual(record.contigs[1].ct[0].date, "123456:765432")
self.assertEqual(
record.contigs[1].ct[0].info,
["This is the forst line of comment for c2", "and this the second for c2"],
["This is the first line of comment for c2", "and this the second for c2"],
)
self.assertEqual(len(record.contigs[1].wa), 1)
self.assertEqual(record.contigs[1].wa[0].tag_type, "phrap_params")
@ -779,7 +779,7 @@ class AceTestOne(unittest.TestCase):
self.assertEqual(contig.ct[0].date, "123456:765432")
self.assertEqual(
contig.ct[0].info,
["This is the forst line of comment for c2", "and this the second for c2"],
["This is the first line of comment for c2", "and this the second for c2"],
)
self.assertEqual(contig.ct[1].name, "unrelated_Contig")
self.assertEqual(contig.ct[1].tag_type, "repeat")
@ -790,7 +790,7 @@ class AceTestOne(unittest.TestCase):
self.assertEqual(
contig.ct[1].info,
[
"This is the forst line of comment for the unrelated ct tag",
"This is the first line of comment for the unrelated ct tag",
"and this the second",
],
)
@ -803,7 +803,7 @@ class AceTestOne(unittest.TestCase):
self.assertEqual(contig.ct[2].date, "555456:555432")
self.assertEqual(
contig.ct[2].info,
["This is the forst line of comment for c1", "and this the second for c1"],
["This is the first line of comment for c1", "and this the second for c1"],
)
self.assertEqual(len(contig.wa), 1)

6
Tests/test_GenBank.py
View File

@ -8041,7 +8041,7 @@ class LineOneTests(unittest.TestCase):
def test_topology_genbank(self):
"""Check GenBank LOCUS line parsing."""
# This is a bit low level,
# but can test pasing the LOCUS line only
# but can test parsing the LOCUS line only
tests = [
("LOCUS U00096", None, None, None, None),
# This example is actually fungal,
@ -8124,7 +8124,7 @@ class LineOneTests(unittest.TestCase):
def test_topology_embl(self):
"""Check EMBL ID line parsing."""
# This is a bit low level, but can test pasing the ID line only
# This is a bit low level, but can test parsing the ID line only
tests = [
# Modern examples with sequence version
(
@ -8190,7 +8190,7 @@ class LineOneTests(unittest.TestCase):
def test_first_line_imgt(self):
"""Check IMGT ID line parsing."""
# This is a bit low level, but can test pasing the ID line only
# This is a bit low level, but can test parsing the ID line only
tests = [
("ID HLA00001 standard; DNA; HUM; 3503 BP.", None, "DNA", "HUM"),
("ID HLA00001; SV 1; standard; DNA; HUM; 3503 BP.", None, "DNA", "HUM"),

2
Tests/test_PAML_codeml.py
View File

@ -279,7 +279,7 @@ class ModTest(unittest.TestCase):
self.assertIn("site-class model", results, version_msg)
self.assertEqual(results["site-class model"], "discrete", version_msg)
self.assertIn("NSsites", results, version_msg)
# There should be 1 NSsites classe: 3
# There should be 1 NSsites class: 3
self.assertEqual(len(results["NSsites"]), 1, version_msg)
# Each site class model should have 5 sub-items: 'lnL', 'tree',
# 'description', 'parameters', & 'tree length'. It should

2
Tests/test_samtools_tool.py
View File

@ -180,7 +180,7 @@ class SamtoolsTestCase(unittest.TestCase):
# print("exists")
stderr_calmd_expected = ""
else:
# print("doesnt exist")
# print("doesn't exist")
stderr_calmd_expected = "[fai_load] build FASTA index.\n"
stdout, stderr = cmdline()
self.assertEqual(stderr, stderr_calmd_expected)