def __init__(self, args, unknown_args):
self.args = args
self.unknown_args = unknown_args
self.option = checkInput(args)
#
env.logger = getLogger(max(min(args.verbosity - 1, 2), 0),
fn=os.path.splitext(args.output[0])[0],
fv=2 if args.verbosity is not 0 else 0)
env.logger.debug('\n{0}\n{1}\n{0}'.format(
"=" * min(len(args.cmd), 100), args.cmd))
self.logger = env.logger.info if args.verbosity != 1 else printinfo
#
self.logger('Loading data from [{}] ...'.format(args.data))
if self.option == 1:
self.file = SFSFile(args.data)
else:
self.file = GFile(args.data)
self.groups = self.file.getnames()
self.logger('{:,d} units found'.format(len(self.groups)))
# load non-missing data
# to annotate to each variant position wether or not it is missing from assocation analysis
# name it chip_file because it mimics the behavior of exome chip design
if args.missing_unlisted:
self.chip_file = SFSFile(args.missing_unlisted)
else:
self.chip_file = None
# set limit
if self.args.limit:
self.limit = min(max(1, args.limit), len(self.groups))
self.logger('{:,d} units will be analyzed'.format(self.limit))
else:
self.limit = len(self.groups)
self.result = ResultManager(args.output,
action='w' if not args.append else 'a')
if self.args.verbosity == 1:
# widgets = [FormatLabel('scanning: unit %(value)d - '), BouncingBar(marker=RotatingMarker())]
widgets = [
FormatLabel('scanning: unit %(value)d - '),
Percentage(), ' ',
Bar('>'), ' ',
ETA()
]
self.pbar = ProgressBar(widgets=widgets,
maxval=self.limit,
term_width=get_terminal_size()[0] -
5).start()
else:
# use each group's progress bar or not progress bar at all
self.pbar = ProgressBarNull()
# this is buffer object to hold all input dict to a list
self.data_buffer = [] if self.args.replicates < 0 else None
def __init__(self, args, unknown_args):
self.args = args
self.unknown_args = unknown_args
self.option = checkInput(args)
#
env.logger = getLogger(
max(min(args.verbosity - 1, 2), 0),
fn=os.path.splitext(args.output[0])[0],
fv=2 if args.verbosity is not 0 else 0,
)
env.logger.debug("\n{0}\n{1}\n{0}".format("=" * min(len(args.cmd), 100), args.cmd))
self.logger = env.logger.info if args.verbosity != 1 else printinfo
#
self.logger("Loading data from [{}] ...".format(args.data))
if self.option == 1:
self.file = SFSFile(args.data)
else:
self.file = GFile(args.data)
self.groups = self.file.getnames()
self.logger("{:,d} units found".format(len(self.groups)))
# load non-missing data
# to annotate to each variant position wether or not it is missing from assocation analysis
# name it chip_file because it mimics the behavior of exome chip design
if args.missing_unlisted:
self.chip_file = SFSFile(args.missing_unlisted)
else:
self.chip_file = None
# set limit
if self.args.limit:
self.limit = min(max(1, args.limit), len(self.groups))
self.logger("{:,d} units will be analyzed".format(self.limit))
else:
self.limit = len(self.groups)
self.result = ResultManager(args.output, action="w" if not args.append else "a")
if self.args.verbosity == 1:
# widgets = [FormatLabel('scanning: unit %(value)d - '), BouncingBar(marker=RotatingMarker())]
widgets = [FormatLabel("scanning: unit %(value)d - "), Percentage(), " ", Bar(">"), " ", ETA()]
self.pbar = ProgressBar(widgets=widgets, maxval=self.limit, term_width=get_terminal_size()[0] - 5).start()
else:
# use each group's progress bar or not progress bar at all
self.pbar = ProgressBarNull()
# this is buffer object to hold all input dict to a list
self.data_buffer = [] if self.args.replicates < 0 else None
def show_gdat():
if '-v2' in unknown_args:
try:
print(runCommand('ptdump {}'.format(fn)))
except:
raise ValueError('Cannot display summary information. Make sure "{}" exists and "ptdump" is installed'.format(fn))
else:
try:
gf = GFile(fn)
names = gf.getnames()
gf.close()
except:
names = []
for idx, name in enumerate(names):
print('/%s' % name)
if idx >= 50 and '-v0' in unknown_args:
remaining = len(names) - 50
if remaining:
printinfo('%s more items not displayed. Use "-v1/-v2" switch to see more.' % remaining)
break
def show_gdat():
if '-v2' in unknown_args:
try:
print(runCommand('ptdump {}'.format(fn)))
except:
raise ValueError(
'Cannot display summary information. Make sure "{}" exists and "ptdump" is installed'
.format(fn))
else:
try:
gf = GFile(fn)
names = gf.getnames()
gf.close()
except:
names = []
for idx, name in enumerate(names):
print('/%s' % name)
if idx >= 50 and '-v0' in unknown_args:
remaining = len(names) - 50
if remaining:
printinfo(
'%s more items not displayed. Use "-v1/-v2" switch to see more.'
% remaining)
break
def showFields(fn, border, unknown_args):
def set_style(pt):
if border == 'less':
pt.set_style(MSWORD_FRIENDLY)
if border == 'no':
pt.set_style(PLAIN_COLUMNS)
#
if fn.endswith('.csv'):
pt = from_csv(openFile(fn), delimiter = ',')
set_style(pt)
header = [x for x in pt.field_names if not x.startswith('_')]
if len(unknown_args) == 0:
print('\n'.join(header))
return
fields = [re.compile(item.replace('*', '(.*?)')) if '*' in item else item for item in unknown_args]
output = []
for item in fields:
if type(item) is str:
item = [x for x in header if x == item]
else:
item = [x for x in header if re.match(item, x)]
output.extend(item)
print pt.get_string(fields=output)
elif fn.endswith('.SEQPowerDB'):
if not os.path.isfile(fn):
raise OSError('Cannot find {}'.format(fn))
rs = ResultManager(fn)
pt = PrettyTable()
set_style(pt)
# show tables
if len(unknown_args) == 0:
pt.add_column('TABLES', rs.get_tables())
print pt
return
table = unknown_args[0]
if table not in rs.get_tables():
raise ValueError("Cannot find table '{}'".format(table))
if '--debug' in unknown_args:
debug = True
unknown_args.pop(unknown_args.index('--debug'))
else:
debug = False
if '--condition' in unknown_args:
fields = unknown_args[1:unknown_args.index('--condition')]
condition = ' '.join(unknown_args[(unknown_args.index('--condition') + 1):])
else:
fields = unknown_args[1:]
condition = None
# show fields
header = sorted(rs.get_fields(table),
key = lambda x: x.replace("_", "|").replace('method', 'AAA').replace('power', 'AAB'))
if len(fields) == 0:
pt.add_column(table,header)
pt.align[table] = "l"
print pt
else:
names = [x for x in fields if x in header]
select_query = "SELECT {} from {} {}".format(','.join(names),
table, condition if condition else '')
if debug:
sys.stderr.write(select_query + '\n')
pt.field_names = names
for item in rs.cur.execute(select_query).fetchall():
pt.add_row(item)
print pt
elif fn.split('.')[-1] in ['gdat', 'h5', 'hdf5']:
def show_gdat():
if '-v2' in unknown_args:
try:
print(runCommand('ptdump {}'.format(fn)))
except:
raise ValueError('Cannot display summary information. Make sure "{}" exists and "ptdump" is installed'.format(fn))
else:
try:
gf = GFile(fn)
names = gf.getnames()
gf.close()
except:
names = []
for idx, name in enumerate(names):
print('/%s' % name)
if idx >= 50 and '-v0' in unknown_args:
remaining = len(names) - 50
if remaining:
printinfo('%s more items not displayed. Use "-v1/-v2" switch to see more.' % remaining)
break
#
if '--from' in unknown_args:
for item in unknown_args[(unknown_args.index('--from') + 1):]:
prefix, surfix = os.path.splitext(os.path.basename(item))
if surfix in ['.gdat', '.h5', '.hdf5']:
runCommand('h5copy -v -i {0} -o {1} -s "/{2}" -d "/{2}"'.format(item, fn, re.sub(r'[^a-zA-Z0-9_]', '_', prefix)), accepted_rc = [0,1])
if not '-v0' in unknown_args:
printinfo('File {} processed!'.format(item))
if '--to' in unknown_args:
target = unknown_args[(unknown_args.index('--to') + 1):]
target = target[0] if target else os.path.splitext(fn)[0]
runCommand('mkdir -p {}'.format(target))
gf = GFile(fn)
names = gf.getnames()
gf.close()
for name in gf.getnames():
dat = GData(fn, name)
if not '-v0' in unknown_args:
printinfo('Saving files {}'.format(os.path.join(target, '{}.*.txt'.format(name))))
dat.decompress()
for key in dat:
np.savetxt(os.path.join(target, '{}.{}.txt'.format(name, key)), dat[key], fmt = '%s', delimiter = '\t')
show_gdat()
else:
raise ValueError('Unsupported file type {}'.format(fn))
return
class Executor:
def __init__(self, args, unknown_args):
self.args = args
self.unknown_args = unknown_args
self.option = checkInput(args)
#
env.logger = getLogger(max(min(args.verbosity - 1, 2), 0), fn = os.path.splitext(args.output[0])[0],
fv = 2 if args.verbosity is not 0 else 0)
env.logger.debug('\n{0}\n{1}\n{0}'.format("="*min(len(args.cmd), 100), args.cmd))
self.logger = env.logger.info if args.verbosity != 1 else printinfo
#
self.logger('Loading data from [{}] ...'.format(args.data))
if self.option == 1:
self.file = SFSFile(args.data)
else:
self.file = GFile(args.data)
self.groups = self.file.getnames()
self.logger('{:,d} units found'.format(len(self.groups)))
# load non-missing data
# to annotate to each variant position wether or not it is missing from assocation analysis
# name it chip_file because it mimics the behavior of exome chip design
if args.missing_unlisted:
self.chip_file = SFSFile(args.missing_unlisted)
else:
self.chip_file = None
# set limit
if self.args.limit:
self.limit = min(max(1, args.limit), len(self.groups))
self.logger('{:,d} units will be analyzed'.format(self.limit))
else:
self.limit = len(self.groups)
self.result = ResultManager(args.output, action = 'w' if not args.append else 'a')
if self.args.verbosity == 1:
# widgets = [FormatLabel('scanning: unit %(value)d - '), BouncingBar(marker=RotatingMarker())]
widgets = [FormatLabel('scanning: unit %(value)d - '), Percentage(), ' ',
Bar('>'), ' ', ETA()]
self.pbar = ProgressBar(widgets=widgets, maxval = self.limit,
term_width=get_terminal_size()[0] - 5).start()
else:
# use each group's progress bar or not progress bar at all
self.pbar = ProgressBarNull()
# this is buffer object to hold all input dict to a list
self.data_buffer = [] if self.args.replicates < 0 else None
def run(self):
if self.data_buffer is not None and self.option == 0:
if self.args.resampling:
self.logger('[WARNING] Loading all genotype data to memory. May fail if there is not enough memory!')
else:
self.logger('Converting data attributes ...')
try:
if self.option == 1:
self.__scan_sfs()
else:
self.__scan_gdat()
except:
self.result.close(quiet = True)
raise
self.file.close()
if self.chip_file is not None:
self.chip_file.close()
if self.data_buffer is not None:
self.result.append(Calculator(self.args, self.unknown_args, self.data_buffer).run())
self.result.close()
self.pbar.finish()
def __scan_gdat(self):
'''scan gdat file'''
maf = 'maf'
pos = 'position'
function_score = 'annotation'
# Allow for customized key names in gdat file
try:
for x, y in zip(getColumn(self.args.data[:-5] + '.key', 1),
getColumn(self.args.data[:-5] + '.key', 2)):
if x == 'maf':
maf = y
if x == 'position':
pos = y
if x == 'annotation':
function_score = y
except:
pass
#
for group, item in enumerate(self.groups):
if group >= self.limit:
break
data = self.file.getdata(item)
if self.args.resampling:
data.decompress()
else:
data['haplotype'] = [[]]
try:
loci_input = {'pool':data['haplotype'], 'name':item,
'maf':list(data[maf]), 'pos':list(data[pos]),
'function_score':list(data[function_score])}
except KeyError as e:
env.logger.error('Column name {} not found. Please provide [{}.key] file to overwrite column naming conventions.'.\
format(e, self.args.data[:-5]))
continue
loci_input['num_variants'] = len(loci_input['maf'])
if self.chip_file:
cdata = self.chip_file.getdata(item)
if cdata is None or (not is_within(cdata['num_variants'], self.args.def_valid_locus)):
continue
loci_input['missing'] = [False if x in cdata['pos'] else True for x in loci_input['pos']]
else:
loci_input['missing'] = None
if is_within(loci_input['num_variants'], self.args.def_valid_locus):
if self.data_buffer is None:
self.result.append(Calculator(self.args, self.unknown_args,loci_input).run())
else:
self.data_buffer.append(loci_input)
self.pbar.update(group + 1)
def __scan_sfs(self):
for group, loci_input in enumerate(self.file.data):
if group >= self.limit:
break
# text sfs file does not have any haplotype pools
loci_input['pool'] = [[]]
if self.chip_file:
cdata = self.chip_file.getdata(loci_input['name'])
if cdata is None or (not is_within(cdata['num_variants'], self.args.def_valid_locus)):
continue
loci_input['missing'] = [False if x in cdata['pos'] else True for x in loci_input['pos']]
assert len(loci_input['missing']) == len(loci_input['maf'])
else:
loci_input['missing'] = None
if is_within(loci_input['num_variants'], self.args.def_valid_locus):
if self.data_buffer is None:
self.result.append(Calculator(self.args, self.unknown_args,loci_input).run())
else:
self.data_buffer.append(loci_input)
self.pbar.update(group + 1)
class Executor:
def __init__(self, args, unknown_args):
self.args = args
self.unknown_args = unknown_args
self.option = checkInput(args)
#
env.logger = getLogger(max(min(args.verbosity - 1, 2), 0),
fn=os.path.splitext(args.output[0])[0],
fv=2 if args.verbosity is not 0 else 0)
env.logger.debug('\n{0}\n{1}\n{0}'.format(
"=" * min(len(args.cmd), 100), args.cmd))
self.logger = env.logger.info if args.verbosity != 1 else printinfo
#
self.logger('Loading data from [{}] ...'.format(args.data))
if self.option == 1:
self.file = SFSFile(args.data)
else:
self.file = GFile(args.data)
self.groups = self.file.getnames()
self.logger('{:,d} units found'.format(len(self.groups)))
# load non-missing data
# to annotate to each variant position wether or not it is missing from assocation analysis
# name it chip_file because it mimics the behavior of exome chip design
if args.missing_unlisted:
self.chip_file = SFSFile(args.missing_unlisted)
else:
self.chip_file = None
# set limit
if self.args.limit:
self.limit = min(max(1, args.limit), len(self.groups))
self.logger('{:,d} units will be analyzed'.format(self.limit))
else:
self.limit = len(self.groups)
self.result = ResultManager(args.output,
action='w' if not args.append else 'a')
if self.args.verbosity == 1:
# widgets = [FormatLabel('scanning: unit %(value)d - '), BouncingBar(marker=RotatingMarker())]
widgets = [
FormatLabel('scanning: unit %(value)d - '),
Percentage(), ' ',
Bar('>'), ' ',
ETA()
]
self.pbar = ProgressBar(widgets=widgets,
maxval=self.limit,
term_width=get_terminal_size()[0] -
5).start()
else:
# use each group's progress bar or not progress bar at all
self.pbar = ProgressBarNull()
# this is buffer object to hold all input dict to a list
self.data_buffer = [] if self.args.replicates < 0 else None
def run(self):
if self.data_buffer is not None and self.option == 0:
if self.args.resampling:
self.logger(
'[WARNING] Loading all genotype data to memory. May fail if there is not enough memory!'
)
else:
self.logger('Converting data attributes ...')
try:
if self.option == 1:
self.__scan_sfs()
else:
self.__scan_gdat()
except:
self.result.close(quiet=True)
raise
self.file.close()
if self.chip_file is not None:
self.chip_file.close()
if self.data_buffer is not None:
self.result.append(
Calculator(self.args, self.unknown_args,
self.data_buffer).run())
self.result.close()
self.pbar.finish()
def __scan_gdat(self):
'''scan gdat file'''
maf = 'maf'
pos = 'position'
function_score = 'annotation'
# Allow for customized key names in gdat file
try:
for x, y in zip(getColumn(self.args.data[:-5] + '.key', 1),
getColumn(self.args.data[:-5] + '.key', 2)):
if x == 'maf':
maf = y
if x == 'position':
pos = y
if x == 'annotation':
function_score = y
except:
pass
#
for group, item in enumerate(self.groups):
if group >= self.limit:
break
data = self.file.getdata(item)
if self.args.resampling:
data.decompress()
else:
data['haplotype'] = [[]]
try:
loci_input = {
'pool': data['haplotype'],
'name': item,
'maf': list(data[maf]),
'pos': list(data[pos]),
'function_score': list(data[function_score])
}
except KeyError as e:
env.logger.error('Column name {} not found. Please provide [{}.key] file to overwrite column naming conventions.'.\
format(e, self.args.data[:-5]))
continue
loci_input['num_variants'] = len(loci_input['maf'])
if self.chip_file:
cdata = self.chip_file.getdata(item)
if cdata is None or (not is_within(cdata['num_variants'],
self.args.def_valid_locus)):
continue
loci_input['missing'] = [
False if x in cdata['pos'] else True
for x in loci_input['pos']
]
else:
loci_input['missing'] = None
if is_within(loci_input['num_variants'],
self.args.def_valid_locus):
if self.data_buffer is None:
self.result.append(
Calculator(self.args, self.unknown_args,
loci_input).run())
else:
self.data_buffer.append(loci_input)
self.pbar.update(group + 1)
def __scan_sfs(self):
for group, loci_input in enumerate(self.file.data):
if group >= self.limit:
break
# text sfs file does not have any haplotype pools
loci_input['pool'] = [[]]
if self.chip_file:
cdata = self.chip_file.getdata(loci_input['name'])
if cdata is None or (not is_within(cdata['num_variants'],
self.args.def_valid_locus)):
continue
loci_input['missing'] = [
False if x in cdata['pos'] else True
for x in loci_input['pos']
]
assert len(loci_input['missing']) == len(loci_input['maf'])
else:
loci_input['missing'] = None
if is_within(loci_input['num_variants'],
self.args.def_valid_locus):
if self.data_buffer is None:
self.result.append(
Calculator(self.args, self.unknown_args,
loci_input).run())
else:
self.data_buffer.append(loci_input)
self.pbar.update(group + 1)
def showFields(fn, border, unknown_args):
def set_style(pt):
if border == 'less':
pt.set_style(MSWORD_FRIENDLY)
if border == 'no':
pt.set_style(PLAIN_COLUMNS)
#
if fn.endswith('.csv'):
pt = from_csv(openFile(fn), delimiter=',')
set_style(pt)
header = [x for x in pt.field_names if not x.startswith('_')]
if len(unknown_args) == 0:
print('\n'.join(header))
return
fields = [
re.compile(item.replace('*', '(.*?)')) if '*' in item else item
for item in unknown_args
]
output = []
for item in fields:
if type(item) is str:
item = [x for x in header if x == item]
else:
item = [x for x in header if re.match(item, x)]
output.extend(item)
print pt.get_string(fields=output)
elif fn.endswith('.SEQPowerDB'):
if not os.path.isfile(fn):
raise OSError('Cannot find {}'.format(fn))
rs = ResultManager(fn)
pt = PrettyTable()
set_style(pt)
# show tables
if len(unknown_args) == 0:
pt.add_column('TABLES', rs.get_tables())
print pt
return
table = unknown_args[0]
if table not in rs.get_tables():
raise ValueError("Cannot find table '{}'".format(table))
if '--debug' in unknown_args:
debug = True
unknown_args.pop(unknown_args.index('--debug'))
else:
debug = False
if '--condition' in unknown_args:
fields = unknown_args[1:unknown_args.index('--condition')]
condition = ' '.join(
unknown_args[(unknown_args.index('--condition') + 1):])
else:
fields = unknown_args[1:]
condition = None
# show fields
header = sorted(rs.get_fields(table),
key=lambda x: x.replace("_", "|").replace(
'method', 'AAA').replace('power', 'AAB'))
if len(fields) == 0:
pt.add_column(table, header)
pt.align[table] = "l"
print pt
else:
names = [x for x in fields if x in header]
select_query = "SELECT {} from {} {}".format(
','.join(names), table, condition if condition else '')
if debug:
sys.stderr.write(select_query + '\n')
pt.field_names = names
for item in rs.cur.execute(select_query).fetchall():
pt.add_row(item)
print pt
elif fn.split('.')[-1] in ['gdat', 'h5', 'hdf5']:
def show_gdat():
if '-v2' in unknown_args:
try:
print(runCommand('ptdump {}'.format(fn)))
except:
raise ValueError(
'Cannot display summary information. Make sure "{}" exists and "ptdump" is installed'
.format(fn))
else:
try:
gf = GFile(fn)
names = gf.getnames()
gf.close()
except:
names = []
for idx, name in enumerate(names):
print('/%s' % name)
if idx >= 50 and '-v0' in unknown_args:
remaining = len(names) - 50
if remaining:
printinfo(
'%s more items not displayed. Use "-v1/-v2" switch to see more.'
% remaining)
break
#
if '--from' in unknown_args:
for item in unknown_args[(unknown_args.index('--from') + 1):]:
prefix, surfix = os.path.splitext(os.path.basename(item))
if surfix in ['.gdat', '.h5', '.hdf5']:
runCommand(
'h5copy -v -i {0} -o {1} -s "/{2}" -d "/{2}"'.format(
item, fn, re.sub(r'[^a-zA-Z0-9_]', '_', prefix)),
accepted_rc=[0, 1])
if not '-v0' in unknown_args:
printinfo('File {} processed!'.format(item))
if '--to' in unknown_args:
target = unknown_args[(unknown_args.index('--to') + 1):]
target = target[0] if target else os.path.splitext(fn)[0]
runCommand('mkdir -p {}'.format(target))
gf = GFile(fn)
names = gf.getnames()
gf.close()
for name in gf.getnames():
dat = GData(fn, name)
if not '-v0' in unknown_args:
printinfo('Saving files {}'.format(
os.path.join(target, '{}.*.txt'.format(name))))
dat.decompress()
for key in dat:
np.savetxt(os.path.join(target,
'{}.{}.txt'.format(name, key)),
dat[key],
fmt='%s',
delimiter='\t')
show_gdat()
else:
raise ValueError('Unsupported file type {}'.format(fn))
return
def showFields(fn, border, unknown_args):
def set_style(pt):
if border == "less":
pt.set_style(MSWORD_FRIENDLY)
if border == "no":
pt.set_style(PLAIN_COLUMNS)
#
if fn.endswith(".csv"):
pt = from_csv(openFile(fn), delimiter=",")
set_style(pt)
header = [x for x in pt.field_names if not x.startswith("_")]
if len(unknown_args) == 0:
print ("\n".join(header))
return
fields = [re.compile(item.replace("*", "(.*?)")) if "*" in item else item for item in unknown_args]
output = []
for item in fields:
if type(item) is str:
item = [x for x in header if x == item]
else:
item = [x for x in header if re.match(item, x)]
output.extend(item)
print pt.get_string(fields=output)
elif fn.endswith(".SEQPowerDB"):
if not os.path.isfile(fn):
raise OSError("Cannot find {}".format(fn))
rs = ResultManager(fn)
pt = PrettyTable()
set_style(pt)
# show tables
if len(unknown_args) == 0:
pt.add_column("TABLES", rs.get_tables())
print pt
return
table = unknown_args[0]
if table not in rs.get_tables():
raise ValueError("Cannot find table '{}'".format(table))
if "--debug" in unknown_args:
debug = True
unknown_args.pop(unknown_args.index("--debug"))
else:
debug = False
if "--condition" in unknown_args:
fields = unknown_args[1 : unknown_args.index("--condition")]
condition = " ".join(unknown_args[(unknown_args.index("--condition") + 1) :])
else:
fields = unknown_args[1:]
condition = None
# show fields
header = sorted(
rs.get_fields(table), key=lambda x: x.replace("_", "|").replace("method", "AAA").replace("power", "AAB")
)
if len(fields) == 0:
pt.add_column(table, header)
pt.align[table] = "l"
print pt
else:
names = [x for x in fields if x in header]
select_query = "SELECT {} from {} {}".format(",".join(names), table, condition if condition else "")
if debug:
sys.stderr.write(select_query + "\n")
pt.field_names = names
for item in rs.cur.execute(select_query).fetchall():
pt.add_row(item)
print pt
elif fn.split(".")[-1] in ["gdat", "h5", "hdf5"]:
def show_gdat():
if "-v2" in unknown_args:
try:
print (runCommand("ptdump {}".format(fn)))
except:
raise ValueError(
'Cannot display summary information. Make sure "{}" exists and "ptdump" is installed'.format(fn)
)
else:
try:
gf = GFile(fn)
names = gf.getnames()
gf.close()
except:
names = []
for idx, name in enumerate(names):
print ("/%s" % name)
if idx >= 50 and "-v0" in unknown_args:
remaining = len(names) - 50
if remaining:
printinfo('%s more items not displayed. Use "-v1/-v2" switch to see more.' % remaining)
break
#
if "--from" in unknown_args:
for item in unknown_args[(unknown_args.index("--from") + 1) :]:
prefix, surfix = os.path.splitext(os.path.basename(item))
if surfix in [".gdat", ".h5", ".hdf5"]:
runCommand(
'h5copy -v -i {0} -o {1} -s "/{2}" -d "/{2}"'.format(
item, fn, re.sub(r"[^a-zA-Z0-9_]", "_", prefix)
),
accepted_rc=[0, 1],
)
if not "-v0" in unknown_args:
printinfo("File {} processed!".format(item))
if "--to" in unknown_args:
target = unknown_args[(unknown_args.index("--to") + 1) :]
target = target[0] if target else os.path.splitext(fn)[0]
runCommand("mkdir -p {}".format(target))
gf = GFile(fn)
names = gf.getnames()
gf.close()
for name in gf.getnames():
dat = GData(fn, name)
if not "-v0" in unknown_args:
printinfo("Saving files {}".format(os.path.join(target, "{}.*.txt".format(name))))
dat.decompress()
for key in dat:
np.savetxt(os.path.join(target, "{}.{}.txt".format(name, key)), dat[key], fmt="%s", delimiter="\t")
show_gdat()
else:
raise ValueError("Unsupported file type {}".format(fn))
return