def remove_mapped_init_tempfiles(pname, samplename_pat,
samplename, fragment='F',
PCR=1,
VERBOSE=0, remove_chunks=False,
only_chunk=None):
'''Remove the part files of multi-threaded mapping to initial patient consensus'''
from hivwholeseq.patients.filenames import get_mapped_to_initial_foldername, \
get_mapped_to_initial_filename
dirname = get_mapped_to_initial_foldername(pname, samplename_pat, PCR=PCR)
prefix = samplename+'_'+fragment
if only_chunk is None:
fns = glob.glob(dirname+prefix+'*_part*') + \
glob.glob(dirname+prefix+'*_unsorted*') + \
glob.glob(dirname+prefix+'_part*') + \
glob.glob(dirname+prefix+'_unsorted*') + \
glob.glob(dirname+prefix+'.sam') + \
glob.glob(dirname+prefix+'*.sam') + \
glob.glob(dirname+prefix+'*.00*.bam')
else:
fns = glob.glob(dirname+prefix+'*_part*_chunk_'+str(only_chunk)+'*') + \
glob.glob(dirname+prefix+'*_unsorted*_chunk_'+str(only_chunk)+'*') + \
glob.glob(dirname+prefix+'_part*_chunk_'+str(only_chunk)+'*') + \
glob.glob(dirname+prefix+'_unsorted*_chunk_'+str(only_chunk)+'*') + \
glob.glob(dirname+prefix+'_chunk_'+str(only_chunk)+'*.sam') + \
glob.glob(dirname+prefix+'_chunk_'+str(only_chunk)+'*.00*.bam')
if remove_chunks:
fns = fns + glob.glob(dirname+prefix+'*_chunk_*.bam')
fns = frozenset(fns)
for fn in fns:
os.remove(fn)
if VERBOSE >= 3:
print 'File removed:', fn
def make_output_folders(pname, samplename, PCR=1, VERBOSE=0):
'''Make the output folders if necessary for hash and map'''
hash_foldername = os.path.dirname(get_initial_hash_filename(pname, 'F0'))
map_foldername = get_mapped_to_initial_foldername(pname, samplename, PCR=PCR)
if not os.path.isdir(hash_foldername):
mkdirs(hash_foldername)
if VERBOSE:
print 'Folder created:', hash_foldername
mkdirs(map_foldername)
if VERBOSE:
print 'Folder created:', map_foldername
