from htsworkflow.util.makebed import make_bed_from_eland_stream, make_description
+LOGGER = logging.getLogger(__name__)
+
def make_bed_for_gerald(eland_dir, output_dir, prefix, database, flowcell):
"""
convert s_[1-8]_eland_result.txt to corresponding bed files
if len(out_files) > 0:
raise RuntimeError("please move old bedfiles")
- logging.info('Processing %s using flowcell id %s' % (eland_dir, flowcell))
+ LOGGER.info('Processing %s using flowcell id %s' % (eland_dir, flowcell))
for pathname in eland_files:
path, name = os.path.split(pathname)
lane = int(name[2])
outname = 's_%d_eland_result.bed' %(lane,)
- logging.info('Converting lane %d to %s' % (lane, outname))
+ LOGGER.info('Converting lane %d to %s' % (lane, outname))
outpathname = os.path.join(eland_dir, outname)
# look up descriptions
return parser
def main(command_line=None):
- logging.basicConfig(level=logging.WARNING)
+ LOGGER.basicConfig(level=logging.WARNING)
if command_line is None:
command_line = sys.argv[1:]