def illumina_files(runobj):
start = time()
# if os.uname()[1] == 'ashipunova.mbl.edu':
# import shutil
# shutil.rmtree('/Users/ashipunova/BPC/py_mbl_sequencing_pipeline/test/data/fastq/illumina_files_test/output/analysis/')
illumina_files = IlluminaFiles(runobj)
illumina_files.split_files(compressed=runobj.compressed)
illumina_files.perfect_reads()
illumina_files.uniq_fa()
elapsed = time() - start
print "illumina_files time = %s" % str(elapsed)
def illumina_files(runobj):
start = time()
illumina_files = IlluminaFiles(runobj)
illumina_files.open_dataset_files()
illumina_files.split_files(compressed = runobj.compressed)
if runobj.do_perfect:
illumina_files.perfect_reads()
else:
illumina_files.partial_overlap_reads()
illumina_files.filter_mismatches()
illumina_files.uniq_fa()
elapsed = (time() - start)
print "illumina_files time = %s" % str(elapsed)
