out_dir = args.outdir + date if args.outdir[
-1] == "/" else args.outdir + "/" + date
os.makedirs(out_dir)
#SETUP variables and OUTPUT samples
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"
# SETUP variables and OUTPUT samples
ref_type = "nuc" if args.rna else "gen"
is_paired = len(args.input) > 1
out_csv = os.path.join(out_dir, ("%s_result.tsv" % date))
out_plot = os.path.join(out_dir, ("%s_coverage_plot.pdf" % date))
# mapping fished file to reference
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
date = datetime.datetime.fromtimestamp(time.time()).strftime('%Y_%m_%d_%H_%M_%S')
out_dir = args.outdir+date if args.outdir[-1] == "/" else args.outdir+"/"+date
os.makedirs(out_dir)
#SETUP variables and OUTPUT samples
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)