def wrapper():
mapper_config = settings.MapperConfig
pre_process_config = settings.PreprocessConfig
bt_config = settings.BowtieConfig
sf_config = settings.SourceFinderConfig
post_process_config = settings.PostprocessConfig
gene_intersect_config = settings.GeneIntersectConfig
for f in glob(mapper_config.reads_dir + "/*.fastq"):
print "\nProcessing reads file %s...\n" % f
root = re.search(".*/(.*)\.fastq", f).group(1).split("_")
barcode = root[-1]
output = "%s/%s_alignments.txt" % (
new_or_existing_dir(mapper_config.alignments_dir),
"_".join(root[:3]))
main(f, barcode, output, pre_process_config, bt_config,
sf_config, post_process_config, gene_intersect_config)
def __init__(self, config):
self.config = config
self.tmp = new_or_existing_dir(self.config.tmp_dir)
