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)
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.load(in_handle)
assert info[0]['lane'] == '1'
assert info[0]['multiplex'][0]['barcode_id'] == 5
os.remove(out_file)
#!/usr/bin/env python
"""Convert Illumina SampleSheet CSV files to the run_info.yaml input file.
This allows running the analysis pipeline without Galaxy, using CSV input
files from Illumina SampleSheet or Genesifter.
Usage:
convert_samplesheet_config.py <input csv>
"""
import sys
from bcbio.illumina import samplesheet
if __name__ == "__main__":
samplesheet.csv2yaml(sys.argv[1])