Mercurial > repos > brenninc > data_manager_tagdust_architecture
diff data_manager/tagdust_architecture_data_manager.py @ 0:e3b3261e5498 draft default tip
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author | brenninc |
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date | Sun, 08 May 2016 04:44:17 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/tagdust_architecture_data_manager.py Sun May 08 04:44:17 2016 -0400 @@ -0,0 +1,113 @@ +#!/usr/bin/env python + +import json +import optparse +import os.path + +def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): + data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) + data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) + data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) + return data_manager_dict + + +def get_param(name, params, default=None, check_tab=True): + value = params.get(name) + print name, value + return check_param(name, value, default=default, check_tab=check_tab) + + +def check_param(name, value, default=None, check_tab=True): + if value in [ None, '', '?' ]: + if default: + print "Using {0} for {1} as no value provided".format( default, name ) + value = default + else: + raise Exception( '{0} is not a valid {1}. You must specify a valid {1}.'.format( value, name ) ) + if check_tab and "\t" in value: + raise Exception( '{0} is not a valid {1}. It may not contain a tab because these are used as seperators by galaxy .'.format( value, name ) ) + return value + + +def createFileBasedOnHmm(hmms): + file_name = "" + bar_code = "no" + for hmm in hmms: + block = hmm["block"].strip() + if not (block[0] in ['R','O','G','B','F','S','P']): + raise Exception( "hmm block {0} is not a valid. It must start with one of ['R','O','G','B','F','S','P'].".format( block ) ) + if block[0] == 'B': + bar_code = "yes" + if block[1] != ':': + raise Exception( "hmm block {0} is not a valid. The second character must be ':'".format( block ) ) + if "\t" in hmm: + raise Exception( "hmm block {0} is not a valid. It may not contain a tab, due to galaxy using tabs as seperators".format( block ) ) + file_name = file_name + block + "_" + file_name = file_name[:-1] + ".txt" + return bar_code, file_name + + +def get_path(galaxy_tool_dir, file_name): + file_path = os.path.join(galaxy_tool_dir, "tagdust_architecture") + if os.path.exists(file_path): + if os.path.isfile(file_path): + raise Exception( "Found a file at {0}, but expecting a directory there".format( file_path ) ) + else: + os.mkdir(file_path) + return os.path.join(file_path, file_name) + + +def writeHmm(hmms, file_path): + with open( file_path, 'w' ) as output_file: + output_file.write("./tagdust") + for i, hmm in enumerate( hmms, 1 ): + output_file.write(" ") + output_file.write(str(-i)) + output_file.write(" ") + output_file.write(hmm["block"]) + output_file.write("\n") + +def main(): + + #Parse Command Line + parser = optparse.OptionParser() + parser.add_option( '--data_table_name', action='store', type="string", default=None, help='path' ) + parser.add_option( '--json_output_file', action='store', type="string", default=None, help='path' ) + (options, args) = parser.parse_args() + + data_table_name = check_param("data_table_name", options.data_table_name) + json_output_file = check_param("json_output_file", options.json_output_file, check_tab=False) + + param_dict = json.loads( open( json_output_file ).read() ) + params = param_dict.get("param_dict") + print "input params:" + print params + + hmms = get_param("hmms", params) + galaxy_tool_dir = get_param("GALAXY_DATA_INDEX_DIR", params) + + data_table_entry = {} + + data_table_entry["barcode"], file_name = createFileBasedOnHmm(hmms) + data_table_entry["path"] = get_path(galaxy_tool_dir, file_name) + writeHmm(hmms, data_table_entry["path"]) + + basename = os.path.basename(data_table_entry["path"]) + filename = os.path.splitext(basename)[0] + data_table_entry["name"] = get_param("name", params, default=filename) + data_table_entry["value"] = get_param("value", params, default=data_table_entry["name"]) + data_table_entry["dbkey"] = get_param("dbkey", params, default=data_table_entry["value"]) + + data_manager_dict = {} + _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) + + print "output:" + print data_manager_dict + # save info to json file + with open( json_output_file, 'wb' ) as output_file: + output_file.write( json.dumps( data_manager_dict ) ) + output_file.write( "\n" ) + + +if __name__ == "__main__": + main()