import os
from glob import glob
from progressbar import RotatingMarker, ProgressBar, SimpleProgress, Bar, Percentage, ETA
def batcher(iterable, n=1):
l = len(iterable)
for ndx in range(0, l, n):
yield iterable[ndx:min(ndx + n, l)]
def yield_fast5_files(input_path, recursive, follow_symlinks=True):
if os.path.isfile(input_path):
yield input_path
return
if recursive:
for root, _, filenames in os.walk(input_path, followlinks=follow_symlinks):
for filename in filenames:
if not filename.endswith('.fast5'): continue
yield os.path.join(root, filename)
else:
for filename in glob(os.path.join(input_path, '*.fast5')):
yield filename
return
def get_fast5_file_list(input_path, recursive, follow_symlinks=True):
# NB this method is provided for compatibility with use cases where
# generator behaviour is not appropriate.
# E.g. where we need to know the file_list length or be able to sample from it
return list(yield_fast5_files(input_path, recursive, follow_symlinks))
def get_progress_bar(num_reads):
bar_format = [RotatingMarker(), " ", SimpleProgress(), Bar(), Percentage(), " ", ETA()]
progress_bar = ProgressBar(maxval=num_reads, widgets=bar_format)
bad_progressbar_version = False
try:
progress_bar.currval
except AttributeError as e:
bad_progressbar_version = True
pass
if bad_progressbar_version:
raise RuntimeError('Wrong progressbar package detected, likely '
'"progressbar2". Please uninstall that package and '
'install "progressbar33" instead.')
return progress_bar.start()
