def make_raw_zip_bundle(cluster):
"""Zip all the raw samples files in one file"""
result_dir = DirectoryPath(cluster.base_dir + "raw_reads")
result_dir.remove()
result_dir.create()
for sample in tqdm(cluster.samples):
subdir = DirectoryPath(result_dir + sample.short_name)
subdir.create()
shutil.copy(sample.raw.fwd, subdir)
shutil.copy(sample.raw.rev, subdir)
result_dir.zip(keep_orig=False)
class FastQC(object):
"""Takes care of running the FastQC program.
See http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Expects version 0.10.1."""
def __init__(self, source, dest=None):
# Basic #
self.source = FASTQ(source)
self.dest = DirectoryPath(dest)
# Default case #
if dest is None:
self.dest = DirectoryPath(self.source.prefix_path + '.fastqc')
def check(self):
assert sh.fastqc('--v', )
def run(self):
if self.dest is None:
sh.fastqc(self.source, '-q')
os.remove(self.source.prefix_path + '_fastqc.zip')
if self.dest is not None:
if self.dest.exists: self.dest.remove()
self.tmp_dir = new_temp_dir()
sh.fastqc(self.source, '-q', '-o', self.tmp_dir)
created_dir = self.tmp_dir + self.source.prefix.split('.')[0] + '_fastqc/'
shutil.move(created_dir, self.dest)
self.tmp_dir.remove()
return self.results
@property
def output_dir(self):
if self.dest is None: return self.source.split('.')[0] + '_fastqc/'
else: return self.dest
@property_cached
def results(self):
results = FastQCResults(self.output_dir)
if not results: self.run()
return results
