def format_commands(self):
samples = []
if self.by_sample:
samples = list(set([basename(x).split("_")[0] for x in self.files]))
else:
samples = list(set(
[basename(x).split(".split")[0] for x in self.files]
))
for sample in samples:
merge = []
for filename in self.files:
if "{}_".format(sample) in filename:
merge += [filename]
pwd = getcwd()
output = self.rebase_file(join(pwd, sample + self.extension))
regex = "\.split\.[a-z]{1,10}?"
try:
match = search(regex, output).group(0)
output = sub(match, "", output)
except AttributeError as err: # no attribute 'group'
raise (err)
combine_files(merge, output)
def format_commands(self):
input_f = join(self.input_root, self.all_reads_name)
output = join(self.output_root, self.assembly_name)
if self.verbose:
print("Combining input files...", file=stderr)
if not self.dry_run:
combine_files(self.files, input_f)
else:
print("Would have combined files if not dry_run...", file=stderr)
job_name = "{}{}".format(self.cluster_options["job_name"],
basename(self.all_reads_name))
command = ("tadpole.sh in={} out={} prealloc=t prefilter=2 "
"mincontig={} mincov={} k={}").format(input_f,
output,
self.mincontig,
self.mincov,
self.kmer_len)
self.commands[job_name] = command
if self.verbose:
print(command, file=stderr)
