def configure(self, title, pipeline_blocks, pipeline_globals,
pipeline_externals, pipeline_allowed_input_data):
self.title = title
self.globals = OptionsHolder('Globals', pipeline_globals)
self.externals = pipeline_externals
self.allowed_input_data = pipeline_allowed_input_data
self.options_holders = []
index = -1
for block in pipeline_blocks:
index += 1
options_holder = OptionsHolder('', block[1])
options_holder.optional = block[3]
options_holder.selected = block[4]
options_holder.command_line = block[0]
options_holder.title = block[2]
options_holder.index = index
self.options_holders.append(options_holder)
for row in csv_reader:
index += 1
if index == 0:
metids = row[1:]
else:
sampleid = row[0]
metvals = row[1:]
minlen = min(len(metids), len(metvals))
write_meta_values(h5, h5writepath, str(sampleid),
metids[0:minlen], metvals[0:minlen],
parameters['overwrite'] == 'yes')
if __name__ == "__main__":
tic()
settings = OptionsHolder(__doc__, ImportMetaSet_options)
settings.description = 'Metadata import'
settings.do = 'yes'
printlog(settings.program_description)
#Parse command line parameters
try:
settings.parse_command_line_args()
except Exception as inst:
printlog('!!! Error in command line parameters: !!!')
printlog(inst)
printlog('\nRun python ' + sys.argv[0] +
' --help for command line options information!')
sys.exit(-1)
parameters = settings.parameters
if parameters['logfile'] != '':
idx = np.argmin(test*ref)
divpoint = mididx[idx]+1
return divpoint
def export(self):
"""
Prepares peak alignment parameter set for export
"""
self.minsegwidth = self.minsegwidth * self.rtrange[1]
self.maxpeakshift = self.maxpeakshift * self.rtrange[1]
if __name__ == "__main__":
tic();
settings=OptionsHolder(__doc__, InternalAlign_options);
settings.description='Profile Alignment';
settings.do='yes';
printlog(settings.program_description);
try:
settings.parse_command_line_args()
except Exception as inst:
printlog('!!! Error in command line parameters: !!!');
printlog(inst);
printlog('\nRun python ' + sys.argv[0] + ' --help for command line options information!');
sys.exit(-1)
parameters = settings.parameters;
if parameters['logfile'] != '':
start_log(parameters['logfile'], overwrite_existing = (parameters['overwrite_logfile'] == 'yes'), verbosity_level = parameters['verbose']);
printlog(settings.program_description, print_enabled = False);
sp_mean = sp_mean + sp
dataidx = np.append(dataidx, j)
except Exception as inst:
printlog(os.path.basename(datasetid) + ": Failed to readin")
printlog(inst)
dataidx = dataidx.astype(int)
datasets = list(map(datasets.__getitem__, (dataidx)))
sp_mean = sp_mean / len(dataidx)
return sp_mean, crt, datasets
if __name__ == "__main__":
tic()
settings = OptionsHolder(__doc__, TICvis_options)
settings.description = 'Intra-Sample Peak Alignment'
settings.do = 'yes'
printlog(settings.program_description)
#Parse command line parameters
try:
settings.parse_command_line_args()
except Exception as inst:
printlog('!!! Error in command line parameters: !!!')
printlog(inst)
printlog('\nRun python ' + sys.argv[0] +
' --help for command line options information!')
sys.exit(-1)
parameters = settings.parameters
if parameters['logfile'] != '':
if self.method == 'tophat':
nsp, nmz = ics.shape
for i in range(nmz):
ics[:, i] = ndimage.white_tophat(ics[:, i], None, self.__se)
ics[ics <= 0] = 0
return ics
def export(self, rtrange):
if self.method == 'tophat':
del self.__se
self.params['frame'] = self.params['frame'] * rtrange[1]
if __name__ == "__main__":
tic()
settings = OptionsHolder(__doc__, NoiseFilter_options)
settings.description = 'Noise Filtering'
settings.do = 'yes'
printlog(settings.program_description)
#Parse command line parameters
try:
settings.parse_command_line_args()
except Exception as inst:
printlog('!!! Error in command line parameters: !!!')
printlog(inst)
printlog('\nRun python ' + sys.argv[0] +
' --help for command line options information!')
sys.exit(-1)
parameters = settings.parameters
if parameters['logfile'] != '':
#---------------------------------------------------------------------------
#Please also inherit your classes from object or its descendants to make the
#following call to the parent class init work:
#def __init__(self):
# super(type(self), self).__init__()
#===========================================================================
#Here the main part of the code which is executed when the module is run starts
if __name__ == "__main__":
tic()
#Start default timer
#Create command line options handler
settings = OptionsHolder(__doc__, cmdline_options)
#Set module short description. <Replace 'Template module' with your description>
settings.description = 'Template module'
settings.do = 'yes' #Legacy. If you do not intend to - just do not run the module
#Print full module description from header. <Can be changed safely to print
#instead of printlog since logging is not initialized yet, but kept for consistency>
printlog(settings.program_description)
#Parse command line parameters
try:
settings.parse_command_line_args()
except Exception as inst:
printlog('!!! Error in command line parameters: !!!')
printlog(inst)
'raw/crtrange',
data=[
np.floor(minrt * self.time_mult),
resrt * self.time_mult,
np.ceil(maxrt * self.time_mult)
])
printlog('Minimal mz: %s' % np.floor(minmass))
printlog('Maximal mz: %s' % np.ceil(maxmass))
printlog('Minimal rt (sec): %s' % np.floor(minrt * self.time_mult))
printlog('Maximal rt (sec): %s' % np.ceil(maxrt * self.time_mult))
if __name__ == "__main__":
tic()
settings = OptionsHolder(__doc__, ImportSet_options)
settings.description = 'Import Raw Data'
printlog(settings.program_description)
#Parse command line parameters
try:
settings.parse_command_line_args()
except Exception as inst:
printlog('!!! Error in command line parameters: !!!')
printlog(inst)
printlog('\nRun python ' + sys.argv[0] +
' --help for command line options information!')
sys.exit(-1)
parameters = settings.parameters
if parameters['logfile'] != '':
start_log(
fpath = os.path.split(output_prefix)[0];
if not os.path.exists(fpath):
os.makedirs(fpath);
export_HTML_view_to_file(dbfilepath, params['h5readpath'], output_prefix, params['h5fullprofile'],
params['plot_width'], params['top_plot_height'], params['bottom_plot_height']);
return
if __name__ == "__main__":
tic();
settings=OptionsHolder(__doc__, Reporting_options);
settings.description='Generating HTML report';
settings.do='yes';
printlog(settings.program_description);
#Parse command line parameters
try:
settings.parse_command_line_args()
except Exception as inst:
printlog('!!! Error in command line parameters: !!!');
printlog(inst);
printlog('\nRun python ' + sys.argv[0] + ' --help for command line options information!');
sys.exit(-1)
parameters = settings.parameters;
if parameters['logfile'] != '':
start_log(parameters['logfile'], overwrite_existing = (parameters['overwrite_logfile'] == 'yes'), verbosity_level = parameters['verbose']);
if not ('no' in params['export_integral_table']):
export_integral_table_to_file(dbfilepath, params['h5readpath'], output_prefix, dataset_names, params['samples'], params['rts'], params['rt_tolerance']);
if not ('no' in params['export_metadata_table']):
export_metadata_table_to_file(dbfilepath, params['h5readpath'], output_prefix, dataset_names, params['samples']);
'''if not ('no' in params['export_all_peaks']):
export_all_peaks_to_file(dbfilepath, params['h5readpath'], output_prefix, dataset_names);
'''
return
if __name__ == "__main__":
tic();
settings=OptionsHolder(__doc__, Exporting_options);
settings.description='Exporting processed data';
settings.do='yes';
printlog(settings.program_description);
#Parse command line parameters
try:
settings.parse_command_line_args()
except Exception as inst:
printlog('!!! Error in command line parameters: !!!');
printlog(inst);
printlog('\nRun python ' + sys.argv[0] + ' --help for command line options information!');
sys.exit(-1)
parameters = settings.parameters;
if parameters['logfile'] != '':
start_log(parameters['logfile'], overwrite_existing = (parameters['overwrite_logfile'] == 'yes'), verbosity_level = parameters['verbose']);
del h5file[i]
def mkdir(self, target):
"""
Make group defined by target
"""
target = abs_hdf5_path(target, self.h5path).rstrip('/')
printlog('Creating group %s' % (target))
if target in self.h5file:
printlog('Error! %s already exists!' % target)
else:
self.h5file.create_group(target)
if __name__ == "__main__":
settings = OptionsHolder(__doc__, Manipulate_options)
settings.description = 'Manipulation of HDF5 file'
settings.do = 'yes'
printlog(settings.program_description)
settings.parse_command_line_args()
parameters = settings.parameters
if parameters['logfile'] != '':
start_log(
parameters['logfile'],
overwrite_existing=(parameters['overwrite_logfile'] == 'yes'))
printlog(settings.program_description, print_enabled=False)
printlog('Started on %s ' % (time.strftime("%a, %d %b %Y at %H:%M:%S")))
printlog(settings.format_parameters())
tic()