def main(argv=None):
"""
Runs the main program.
:param argv: The command line arguments.
:return: The return code for the program's termination.
"""
args, ret = parse_cmdline(argv)
if ret != GOOD_RET or args is None:
return ret
found_files = find_files_by_dir(args.base_dir, args.pattern)
print("Found {} dirs with files to combine".format(len(found_files)))
for f_dir, files in found_files.items():
if not files:
logger.warn("No files with pattern '{}' found for dir '{}'".format(args.pattern, f_dir))
continue
combo_file = os.path.join(f_dir, args.target_file)
if os.path.exists(combo_file) and not args.overwrite:
warning("Target file already exists: '{}' \n"
"Skipping dir '{}'".format(combo_file, f_dir))
continue
combo = combine([os.path.join(f_dir, tgt) for tgt in files])
write_combo(extract_header(os.path.join(f_dir, files[0])), combo, combo_file)
return GOOD_RET # success
def main(argv=None):
""" Runs the main program.
:param argv: The command line arguments.
:return: The return code for the program's termination.
"""
args, ret = parse_cmdline(argv)
if ret != GOOD_RET or args is None:
return ret
kbt = calc_kbt(args.temp)
if args.src_file is not None:
proc_data = to_zero_point(calc_rad(args.src_file, kbt))
write_csv(proc_data, create_out_fname(args.src_file, prefix=OUT_PFX), RAD_KEY_SEQ)
else:
found_files = find_files_by_dir(args.base_dir, args.pattern)
logger.debug("Found '{}' dirs with files to process".format(len(found_files)))
# noinspection PyCompatibility
for f_dir, files in found_files.iteritems():
if not files:
logger.warn("No files found for dir '{}'".format(f_dir))
continue
for pmf_path in ([os.path.join(f_dir, tgt) for tgt in files]):
proc_data = to_zero_point(calc_rad(pmf_path, kbt))
f_name = create_out_fname(pmf_path, prefix=OUT_PFX)
if allow_write(f_name, overwrite=args.overwrite):
write_csv(proc_data, f_name, RAD_KEY_SEQ)
return GOOD_RET # success
def main(argv=None):
""" Runs the main program.
@param argv: The command line arguments.
:return: The return code for the program's termination.
"""
args, ret = parse_cmdline(argv)
if ret != 0:
return ret
if args.src_file is not None:
proc_data = calc_for_wham(args.src_file)
write_csv(proc_data, create_out_fname(args.src_file, prefix=OUT_PFX),
COLVAR_WHAM_KEY_SEQ)
else:
found_files = find_files_by_dir(args.base_dir, args.pattern)
logger.debug("Found '%d' dirs with files to process", len(found_files))
# noinspection PyCompatibility
for f_dir, files in found_files.iteritems():
if not files:
logger.warn("No files found for dir '%s'", f_dir)
continue
for colvar_path in ([os.path.join(f_dir, tgt) for tgt in files]):
proc_data = calc_for_wham(colvar_path)
f_name = create_out_fname(colvar_path, prefix=OUT_PFX)
if allow_write(f_name, overwrite=args.overwrite):
list_to_file([str(d['r']) for d in proc_data if 'r' in d],
f_name)
# write_csv(proc_data, f_name, COLVAR_WHAM_KEY_SEQ, extrasaction="ignore")
return 0 # success
def main(argv=None):
"""
Runs the main program.
:param argv: The command line arguments.
:return: The return code for the program's termination.
"""
args, ret = parse_cmdline(argv)
if ret != GOOD_RET or args is None:
return ret
found_files = find_files_by_dir(args.base_dir, args.pattern)
print("Found {} dirs with files to combine".format(len(found_files)))
for f_dir, files in found_files.items():
if not files:
logger.warn("No files with pattern '{}' found for dir '{}'".format(
args.pattern, f_dir))
continue
combo_file = os.path.join(f_dir, args.target_file)
if os.path.exists(combo_file) and not args.overwrite:
warning("Target file already exists: '{}' \n"
"Skipping dir '{}'".format(combo_file, f_dir))
continue
combo = combine([os.path.join(f_dir, tgt) for tgt in files])
write_combo(extract_header(os.path.join(f_dir, files[0])), combo,
combo_file)
return GOOD_RET # success
def main(argv=None):
""" Runs the main program.
:param argv: The command line arguments.
:return: The return code for the program's termination.
"""
args, ret = parse_cmdline(argv)
if ret != GOOD_RET or args is None:
return ret
kbt = calc_kbt(args.temp)
if args.src_file is not None:
proc_data = to_zero_point(calc_rad(args.src_file, kbt))
write_csv(proc_data, create_out_fname(args.src_file, prefix=OUT_PFX),
RAD_KEY_SEQ)
else:
found_files = find_files_by_dir(args.base_dir, args.pattern)
logger.debug("Found '{}' dirs with files to process".format(
len(found_files)))
# noinspection PyCompatibility
for f_dir, files in found_files.items():
if not files:
logger.warn("No files found for dir '{}'".format(f_dir))
continue
for pmf_path in ([os.path.join(f_dir, tgt) for tgt in files]):
proc_data = to_zero_point(calc_rad(pmf_path, kbt))
f_name = create_out_fname(pmf_path, prefix=OUT_PFX)
if allow_write(f_name, overwrite=args.overwrite):
write_csv(proc_data, f_name, RAD_KEY_SEQ)
return GOOD_RET # success
def main(argv=None):
""" Runs the main program.
@param argv: The command line arguments.
:return: The return code for the program's termination.
"""
args, ret = parse_cmdline(argv)
if ret != 0:
return ret
if args.src_file is not None:
proc_data = calc_for_wham(args.src_file)
write_csv(proc_data, create_out_fname(args.src_file, prefix=OUT_PFX), COLVAR_WHAM_KEY_SEQ)
else:
found_files = find_files_by_dir(args.base_dir, args.pattern)
logger.debug("Found '%d' dirs with files to process", len(found_files))
# noinspection PyCompatibility
for f_dir, files in found_files.iteritems():
if not files:
logger.warn("No files found for dir '%s'", f_dir)
continue
for colvar_path in ([os.path.join(f_dir, tgt) for tgt in files]):
proc_data = calc_for_wham(colvar_path)
f_name = create_out_fname(colvar_path, prefix=OUT_PFX)
if allow_write(f_name, overwrite=args.overwrite):
list_to_file([str(d['r']) for d in proc_data if 'r' in d], f_name)
# write_csv(proc_data, f_name, COLVAR_WHAM_KEY_SEQ, extrasaction="ignore")
return 0 # success
def main(argv=None):
# Read input
args, ret = parse_cmdline(argv)
if ret != GOOD_RET or args is None:
return ret
cfg = args.config
try:
if args.src_file is not None:
process_file(args.src_file, cfg, delimiter=args.delimiter)
else:
found_files = find_files_by_dir(args.base_dir, cfg[FILE_PAT])
# noinspection PyCompatibility
for f_dir, files in list(found_files.items()):
if not files:
warning("No files found for dir '{}'".format(f_dir))
continue
for csv_path in ([os.path.join(f_dir, tgt) for tgt in files]):
process_file(csv_path, cfg, delimiter=args.delimiter)
except IOError as e:
warning("Problems reading file:", e)
return IO_ERROR
except (ValueError, InvalidDataError) as e:
warning("Problems reading data:", e)
return INVALID_DATA
return GOOD_RET # success
def test_headers(self):
test_dict = find_files_by_dir(FES_OUT_SINGLE, DEF_FILE_PAT)
self.assertEqual(1, len(test_dict))
f_dir, files = test_dict.popitem()
headers = extract_header(os.path.join(f_dir, files[0]))
ref_headers = header_lines(HEADER_DIR)
self.assertEqual(len(headers), len(ref_headers))
self.assertListEqual(ref_headers, headers)
def test_headers(self):
test_dict = find_files_by_dir(FES_OUT_SINGLE, DEF_FILE_PAT)
self.assertEqual(1, len(test_dict))
f_dir, files = test_dict.popitem()
headers = extract_header(os.path.join(f_dir, files[0]))
ref_headers = header_lines(HEADER_DIR)
self.assertEqual(len(headers), len(ref_headers))
self.assertListEqual(ref_headers, headers)
def test_writer(self):
test_dict = find_files_by_dir(FES_OUT_MULTI, DEF_FILE_PAT)
self.assertEqual(1, len(test_dict))
f_dir, files = test_dict.popitem()
combo = combine([os.path.join(f_dir, tgt) for tgt in files])
try:
write_combo(extract_header(os.path.join(f_dir, files[0])), combo, FES_ALL_MULTI_FILE)
self.assertEqual(map_fes(FES_ALL_MULTI), map_fes(FES_ALL_MULTI_FILE))
finally:
os.remove(FES_ALL_MULTI_FILE)
def test_find(self):
found = find_files_by_dir(FES_DIR, DEF_FILE_PAT)
exp_data = expected_dir_data()
self.assertEqual(len(exp_data), len(found))
for key, files in exp_data.items():
found_files = found.get(key)
try:
# noinspection PyUnresolvedReferences
self.assertCountEqual(files, found_files)
except AttributeError:
self.assertItemsEqual(files, found_files)
def test_find(self):
found = find_files_by_dir(FES_DIR, DEF_FILE_PAT)
exp_data = expected_dir_data()
self.assertEqual(len(exp_data), len(found))
for key, files in exp_data.items():
found_files = found.get(key)
try:
# noinspection PyUnresolvedReferences
self.assertCountEqual(files, found_files)
except AttributeError:
self.assertItemsEqual(files, found_files)
def test_writer(self):
test_dict = find_files_by_dir(FES_OUT_MULTI, DEF_FILE_PAT)
self.assertEqual(1, len(test_dict))
f_dir, files = test_dict.popitem()
combo = combine([os.path.join(f_dir, tgt) for tgt in files])
try:
write_combo(extract_header(os.path.join(f_dir, files[0])), combo,
FES_ALL_MULTI_FILE)
self.assertEqual(map_fes(FES_ALL_MULTI),
map_fes(FES_ALL_MULTI_FILE))
finally:
os.remove(FES_ALL_MULTI_FILE)
def main(argv=None):
""" Runs the main program.
:param argv: The command line arguments.
:return: The return code for the program's termination.
"""
args, ret = parse_cmdline(argv)
if ret != GOOD_RET:
return ret
kbt = calc_kbt(args.temp)
if args.coord_ts is not None:
logger.info("Read TS coordinate value: '{:8.3f}'".format(args.coord_ts))
try:
if args.src_file is not None:
file_data = read_csv(args.src_file, data_conv=KEY_CONV)
f_base_name = os.path.basename(args.src_file)
try:
pka, cur_corr, cur_coord = calc_pka(file_data, kbt, args.coord_ts)
result = [{SRC_KEY: f_base_name, PKA_KEY: pka, MAX_VAL: cur_corr, MAX_LOC: cur_coord}]
except NoMaxError:
result = [{SRC_KEY: f_base_name, PKA_KEY: NO_MAX_RET, MAX_VAL: NO_MAX_RET, MAX_LOC: NO_MAX_RET}]
write_result(result, args.src_file, args.overwrite)
else:
found_files = find_files_by_dir(args.base_dir, args.pattern)
logger.debug("Found '{}' dirs with files to process".format(len(found_files)))
if len(found_files) == 0:
raise IOError("No files found in specified directory '{}'".format(args.base_dir))
for f_dir, files in found_files.items():
results = []
for pmf_path, fname in ([(os.path.join(f_dir, tgt), tgt) for tgt in sorted(files)]):
file_data = read_csv(pmf_path, data_conv=KEY_CONV)
try:
pka, cur_corr, cur_coord = calc_pka(file_data, kbt, args.coord_ts)
results.append({SRC_KEY: fname, PKA_KEY: pka, MAX_VAL: cur_corr, MAX_LOC: cur_coord})
except NoMaxError:
results.append({SRC_KEY: fname, PKA_KEY: NO_MAX_RET, MAX_VAL: NO_MAX_RET,
MAX_LOC: NO_MAX_RET})
write_result(results, os.path.basename(f_dir), args.overwrite,
basedir=os.path.dirname(f_dir))
except IOError as e:
warning(e)
return IO_ERROR
return GOOD_RET # success
def main(argv=None):
""" Runs the main program.
:param argv: The command line arguments.
:return: The return code for the program's termination.
"""
args, ret = parse_cmdline(argv)
if ret != GOOD_RET:
return ret
found_files = find_files_by_dir(args.base_dir, args.pattern)
logger.debug("Found '{}' dirs with files to process".format(len(found_files)))
for f_dir, files in found_files.items():
bin_pfx = bin_by_pattern(files)
for pfx, bin_f in bin_pfx.items():
bin_results = calc_avg_stdev([os.path.join(f_dir, tgt) for tgt in bin_f])
avg_fname = OUT_FNAME_FMT.format(pfx)
write_avg_stdev(bin_results, os.path.join(f_dir, avg_fname), overwrite=args.overwrite)
return GOOD_RET # success
def main(argv=None):
"""
Runs the main program.
:param argv: The command line arguments.
:return: The return code for the program's termination.
"""
args, ret = parse_cmdline(argv)
if ret != GOOD_RET or args is None:
return ret
try:
for meta_dir, meta_files in find_files_by_dir(args.base_dir, args.pattern).items():
for meta_file in meta_files:
block_average(os.path.join(meta_dir, meta_file), args.steps, overwrite=args.overwrite)
except TemplateNotReadableError as e:
warning(e)
return INVALID_DATA
return GOOD_RET # success
def main(argv=None):
"""
Runs the main program.
:param argv: The command line arguments.
:return: The return code for the program's termination.
"""
args, ret = parse_cmdline(argv)
if ret != GOOD_RET or args is None:
return ret
try:
for meta_dir, meta_files in find_files_by_dir(args.base_dir, args.pattern).items():
for meta_file in meta_files:
block_average(os.path.join(meta_dir, meta_file), args.steps, overwrite=args.overwrite)
except TemplateNotReadableError as e:
warning(e)
return INVALID_DATA
return GOOD_RET # success
def test_multi(self):
test_dict = find_files_by_dir(FES_OUT_MULTI, DEF_FILE_PAT)
self.assertEqual(1, len(test_dict))
f_dir, files = test_dict.popitem()
combo = combine([os.path.join(f_dir, tgt) for tgt in files])
self.assertDictEqual(map_fes(FES_ALL_MULTI)[1], combo)
def test_multi(self):
test_dict = find_files_by_dir(FES_OUT_MULTI, DEF_FILE_PAT)
self.assertEqual(1, len(test_dict))
f_dir, files = test_dict.popitem()
combo = combine([os.path.join(f_dir, tgt) for tgt in files])
self.assertDictEqual(map_fes(FES_ALL_MULTI)[1], combo)