try:
os.mkdir(
os.path.join(env["BASECALLER_RESULTS"],
"unfiltered.untrimmed"))
basecaller.merge_datasets_basecaller_json(
dirs,
os.path.join(env["BASECALLER_RESULTS"],
"unfiltered.untrimmed"),
)
blockprocessing.merge_bams(
dirs,
os.path.join(env["BASECALLER_RESULTS"],
"unfiltered.untrimmed"),
basecaller_datasets,
"picard",
)
except Exception:
print(traceback.format_exc())
try:
os.mkdir(
os.path.join(env["BASECALLER_RESULTS"],
"unfiltered.trimmed"))
basecaller.merge_datasets_basecaller_json(
dirs,
os.path.join(env["BASECALLER_RESULTS"],
"unfiltered.trimmed"))
printtime("ERROR: merging rawtf.basecaller.bam unsuccessful")
if do_unfiltered_processing:
basecaller_datasets = blockprocessing.get_datasets_basecaller(env['BASECALLER_RESULTS'])
try:
os.mkdir(os.path.join(env['BASECALLER_RESULTS'],'unfiltered.untrimmed'))
basecaller.merge_datasets_basecaller_json(
dirs,
os.path.join(env['BASECALLER_RESULTS'],"unfiltered.untrimmed"))
blockprocessing.merge_bams(
dirs,
os.path.join(env['BASECALLER_RESULTS'],"unfiltered.untrimmed"),
basecaller_datasets,
'picard')
except:
print traceback.format_exc()
try:
os.mkdir(os.path.join(env['BASECALLER_RESULTS'],'unfiltered.trimmed'))
basecaller.merge_datasets_basecaller_json(
dirs,
os.path.join(env['BASECALLER_RESULTS'],"unfiltered.trimmed"))
blockprocessing.merge_bams(
dirs,
printtime("ERROR: merging rawtf.basecaller.bam unsuccessful")
if do_unfiltered_processing:
basecaller_datasets = blockprocessing.get_datasets_basecaller(env['BASECALLER_RESULTS'])
try:
os.mkdir(os.path.join(env['BASECALLER_RESULTS'], 'unfiltered.untrimmed'))
basecaller.merge_datasets_basecaller_json(
dirs,
os.path.join(env['BASECALLER_RESULTS'], "unfiltered.untrimmed"))
blockprocessing.merge_bams(
dirs,
os.path.join(env['BASECALLER_RESULTS'], "unfiltered.untrimmed"),
basecaller_datasets,
'picard')
except:
print traceback.format_exc()
try:
os.mkdir(os.path.join(env['BASECALLER_RESULTS'], 'unfiltered.trimmed'))
basecaller.merge_datasets_basecaller_json(
dirs,
os.path.join(env['BASECALLER_RESULTS'], "unfiltered.trimmed"))
blockprocessing.merge_bams(
dirs,
os.path.join(env['BASECALLER_RESULTS'], "unfiltered.trimmed"),