if not bam_input:
threads = get_num_threads(config.getint("mapping", "threads"))
if VERBOSE:
print("\nmapping with %s threads..." % threads)
for (i, sample), outbam in zip(enumerate(args.input), bam_paths):
if VERBOSE:
print(
"\n", ht.now(), "Mapping %s to %s reference..." %
(os.path.basename(sample), ref_type.upper()))
subprocess.call(MAPPING_CMD %
(threads, outbam, MAPPING_REF[ref_type], sample),
shell=True)
# sam-to-hdf5
table, features = ht.load_hdf(ALLELE_HDF, False, 'table', 'features')
if VERBOSE:
print("\n", ht.now(), "Generating binary hit matrix.")
if is_paired:
# combine matrices for paired-end mapping
pos, read_details = ht.pysam_to_hdf(bam_paths[0])
binary1 = np.sign(pos) # dtype=np.uint16
pos2, read_details2 = ht.pysam_to_hdf(bam_paths[1])
binary2 = np.sign(pos2) # dtype=np.uint16
if not bam_input and config.getboolean('behavior', 'deletebam'):
os.remove(bam_paths[0])
os.remove(bam_paths[1])
ref_type = "nuc" if args.rna else "gen"
is_paired = len(args.input) > 1
out_csv = out_dir+"/%s_result.tsv"%date
out_plot = out_dir+"/%s_coverage_plot.pdf"%date
#mapping fished file to reference
for i, sample in enumerate(args.input):
if args.verbose:
print "\n", ht.now(), "Mapping %s to %s reference..."%(os.path.basename(sample), ref_type.upper())
sample_out = out_dir+"/"+date+"_"+str(i)
subprocess.call(MAPPING_CMD%(config.get("MAPPING", "THREADS"), sample_out,
MAPPING_REF[ref_type], sample), shell=True)
#sam-to-hd5
table, features = ht.load_hdf(ALLELE_HDF, False, 'table', 'features')
if args.verbose:
print "\n", ht.now(), "Generating binary hit matrix."
if is_paired:
#combine matrices for paired-end mapping
sample_1 = out_dir+"/"+date+"_0.sam"
sample_2 = out_dir+"/"+date+"_1.sam"
pos, etc, desc = ht.sam_to_hdf(sample_1, verbosity=args.verbose)
binary1 = pos.applymap(bool).applymap(int)
pos2, etc2, desc2 = ht.sam_to_hdf(sample_2, verbosity=args.verbose)
binary2 = pos2.applymap(bool).applymap(int)
id1 = set(binary1.index)
id2 = set(binary2.index)
