def run(self):
# Combine reads but in fastq format this time #
paths = [sample.renamed for sample in self.cluster]
shell_output("cat %s > %s" % (" ".join(paths), self.reads))
# Clean #
shutil.rmtree(self.p.clusters_dir)
# Run command #
cdhit = sh.Command(cdhit_script)
cdhit("-i", self.reads, "-o", self.p.clusters_dir, "-p", TmpFile.from_string("[ACTG]"))
# Create the centers file with good names #
self.cdhit_centers.rename_with_num("OTU-", self.centers)
def split(self):
# Call Roche binary #
barcode_file = TmpFile.from_string(self.barcode_text)
sh.sfffile("-s", "barcodes_keyword", "-mcf", barcode_file.path, self.path)
# Check result #
produced_files = set(sh.glob('454Reads.*.sff'))
expected_files = set(['454Reads.%s.sff' % (sample.name.upper()) for sample in self.sample_links.values()])
assert produced_files == expected_files
# Make piece objects #
self.pieces = [SamplePiece(p, self) for p in sh.glob('454Reads.*.sff')]
for piece in self.pieces: piece.rename()
# Cleanup #
barcode_file.remove()
