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from ont_fast5_api.fast5_file import Fast5File, Fast5FileTypeError
from ont_fast5_api.fast5_info import _clean
from ont_fast5_api.multi_fast5 import MultiFast5File
MULTI_READ = "multi-read"
SINGLE_READ = "single-read"
BULK_FAST5 = "bulk"
def get_fast5_file(filepath, mode='r', driver=None):
if is_multi_read(filepath):
return MultiFast5File(filepath, mode, driver=driver)
else:
return Fast5File(filepath, mode)
def check_file_type(f5_file):
try:
return _clean(f5_file.handle.attrs['file_type'])
except KeyError:
# On older files we don't have the 'file_type' attribute so check groups explicitly
if len(f5_file.handle) == 0:
# If there are no top-level groups we default to MultiRead
return MULTI_READ
if len([read for read in f5_file.handle if read.startswith('read_')]) != 0:
# If there are any read_xxx groups we're definitely MultiRead
return MULTI_READ
if "UniqueGlobalKey" in f5_file.handle:
# This group indicates a single read
return SINGLE_READ
raise TypeError("Fast5 file type could not be identified as single- or multi-read. "
"\nFilepath: {}".format(f5_file.filename))
def is_multi_read(filepath):
"""
Determine if a file is a MultiFast5File, True if it is, False if it is a single Fast5File error for other types
"""
with MultiFast5File(filepath, mode='r') as f5_file:
file_type = check_file_type(f5_file)
if file_type == MULTI_READ:
return True
elif file_type == SINGLE_READ:
return False
elif file_type == BULK_FAST5:
raise NotImplementedError("ont_fast5_api does not support bulk fast files: {}".format(filepath))
raise Fast5FileTypeError("Unknown file type: '{}' for file: {}".format(file_type, filepath))
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