def get_read_file_type(input_filename, log=None):
if input_filename in options_storage.dict_of_prefixes:
ext = options_storage.dict_of_prefixes[input_filename]
file_type = SeqIO.get_read_file_type("filename" + ext)
else:
file_type = SeqIO.get_read_file_type(input_filename)
if not file_type:
error("incorrect extension of reads file: %s" % input_filename, log)
return file_type
def get_max_reads_length(reads_file, log, num_checked):
if reads_file in options_storage.dict_of_prefixes:
ext = options_storage.dict_of_prefixes[reads_file]
file_type = SeqIO.get_read_file_type(ext)
else:
file_type = SeqIO.get_read_file_type(reads_file)
if not file_type:
error("incorrect extension of reads file: %s" % reads_file, log)
max_reads_length = max([
len(rec) for rec in itertools.islice(
SeqIO.parse(SeqIO.Open(reads_file, "r"), file_type), num_checked)
])
log.info("%s: max reads length: %s" % (reads_file, str(max_reads_length)))
return max_reads_length
def get_max_reads_length(reads_file, log, num_checked):
file_type = SeqIO.get_read_file_type(reads_file)
if not file_type:
error('Incorrect extension of reads file: ' + reads_file, log)
max_reads_length = max([len(rec) for rec in itertools.islice(SeqIO.parse(SeqIO.Open(reads_file, "r"), file_type), num_checked)])
log.info(reads_file + ': max reads length: ' + str(max_reads_length))
return max_reads_length