def write_full_mapping_file(study, study_input_dir,zip_fname,files_to_remove,
output_dir):
""" Generate a merged mapping file """
# write per_run mapping files and then return the prefixes
run_prefixes=write_db_mapping_files(study,True,study_input_dir,False)
# define the full mapping file
mapping_fname='study_%s_mapping_file.txt' % (str(study))
final_mapping_fp=join(output_dir,mapping_fname)
# add to list of files to remove
files_to_remove.append(final_mapping_fp)
# iterate over run_prefixes and create a list of files that need to be
# merged
mapping_files_to_merge=[]
for i in run_prefixes:
mapping_fp=join(study_input_dir,'study_%s_run_%s_mapping.txt' % \
(str(study),str(i)))
# add to list of files to remove
files_to_remove.append(mapping_fp)
mapping_files_to_merge.append(open(mapping_fp,'U'))
# merge the mapping files and return tabular data
mapping_data = merge_mapping_files(mapping_files_to_merge,\
no_data_value='no_data')
# write the full mapping file
write_mapping_file(mapping_data,final_mapping_fp)
# zip the full mapping file
#cmd_call='cd %s; tar czvf %s %s' % (study_input_dir,zip_fname,mapping_fname)
#system(cmd_call)
return files_to_remove
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
verbose = opts.verbose
output_fp = opts.output_fp
mapping_files = [open(fp,'U') for fp in opts.mapping_fps]
no_data_value = opts.no_data_value
mapping_data = merge_mapping_files(mapping_files,\
no_data_value=no_data_value)
write_mapping_file(mapping_data,output_fp)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
verbose = opts.verbose
output_fp = opts.output_fp
mapping_files = [open(fp, 'U') for fp in opts.mapping_fps]
no_data_value = opts.no_data_value
mapping_data = merge_mapping_files(mapping_files,
no_data_value=no_data_value)
write_mapping_file(mapping_data, output_fp)
