def test_missing_fai_error_message(self):
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
inFas = os.path.join(outdir, 'infile.fasta')
# copy fasta reference to hide fai and ensure FastaReader is used
shutil.copyfile(
ReferenceSet(data.getXml(8)).toExternalFiles()[0], inFas)
rs1 = ContigSet(inFas)
with pytest.raises(IOError) as cm:
rs1.assertIndexed()
assert str(cm) == (
"Companion FASTA index (.fai) file not found or malformatted! "
"Use 'samtools faidx' to generate FASTA index.")
def test_missing_fai_error_message(self):
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
inFas = os.path.join(outdir, 'infile.fasta')
# copy fasta reference to hide fai and ensure FastaReader is used
backticks('cp {i} {o}'.format(
i=ReferenceSet(data.getXml(9)).toExternalFiles()[0],
o=inFas))
rs1 = ContigSet(inFas)
with self.assertRaises(IOError) as cm:
rs1.assertIndexed()
self.assertEqual(
str(cm.exception),
( "Companion FASTA index (.fai) file not found or malformatted! "
"Use 'samtools faidx' to generate FASTA index."))
def test_missing_fai_error_message(self):
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
inFas = os.path.join(outdir, 'infile.fasta')
# copy fasta reference to hide fai and ensure FastaReader is used
backticks('cp {i} {o}'.format(i=ReferenceSet(
data.getXml(9)).toExternalFiles()[0],
o=inFas))
rs1 = ContigSet(inFas)
with self.assertRaises(IOError) as cm:
rs1.assertIndexed()
self.assertEqual(
str(cm.exception),
("Companion FASTA index (.fai) file not found or malformatted! "
"Use 'samtools faidx' to generate FASTA index."))
def n_reads_in_contigset(contigset_file):
"""Return number of reads in a contigset"""
cs = ContigSet(contigset_file)
cs.assertIndexed()
return int(cs.numRecords)
