def writeSammpleSheets(sample_list, sheet_path, template_sheet):
samplesheet_name = os.path.basename(sheet_path)
samplesheet_dir = os.path.dirname(os.path.realpath(sheet_path))
count = 0
exit_status = "success"
for key in sample_list:
count += 1
logger.debug(
f"{len(sample_list[key])} samples with idx lengths {key[1]}/{key[2]} for {key[0]} dataset"
)
new_sample_sheet = SampleSheet()
new_sample_sheet.Header = template_sheet.Header
new_sample_sheet.Reads = template_sheet.Reads
new_sample_sheet.Settings = template_sheet.Settings
for sample in sample_list[key]:
new_sample_sheet.add_sample(sample)
new_sample_sheet_file = os.path.join(
samplesheet_dir,
samplesheet_name + ".custom." + str(count) + "." + key[0])
logger.info(f"Creating custom sample sheet: {new_sample_sheet_file}")
try:
with open(new_sample_sheet_file, "w") as ss_writer:
new_sample_sheet.write(ss_writer)
except Exception as error:
logger.error(f"Exception writing new sample sheet: {error}")
exit_status = "failure"
logger.debug(f"Created custom sample sheet: {new_sample_sheet_file}")
return exit_status
def to_csv(sample_sheet: SampleSheet) -> str:
with io.StringIO() as sio:
sample_sheet.write(sio)
return sio.getvalue()
