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