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"""Tests associated with detecting sequencing results dumped from a machine.
"""
import os
import yaml
import pytest
from bcbio.illumina import samplesheet
class TestSampleSheet(object):
"""Deal with Illumina SampleSheets and convert to YAML input.
"""
@property
def ss_file(self):
return os.path.join(
os.path.dirname(os.path.dirname(__file__)),
"data", "illumina_samplesheet.csv")
@pytest.mark.speed1
def test_toyaml(self):
"""Convert CSV Illumina SampleSheet to YAML.
"""
out_file = samplesheet.csv2yaml(self.ss_file)
assert os.path.exists(out_file)
with open(out_file) as in_handle:
info = yaml.safe_load(in_handle)
assert info[0]['lane'] == '1'
assert info[0]['multiplex'][0]['barcode_id'] == 5
os.remove(out_file)
@pytest.mark.speed1
def test_checkforrun(self):
"""Check for the presence of runs in an Illumina SampleSheet.
"""
fcdir = "fake/101007_80HM7ABXX"
config = {"samplesheet_directories": [os.path.dirname(self.ss_file)]}
ss = samplesheet.run_has_samplesheet(fcdir, config, False)
assert ss is not None
fcdir = "fake/101007_NOPEXX"
ss = samplesheet.run_has_samplesheet(fcdir, config, False)
assert ss is None
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