Mercurial > repos > iuc > data_manager_metaphlan_database_downloader

comparison data_manager/data_manager_metaphlan_download.py @ 2:5fe20c915fa6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
author iuc
date Tue, 28 Mar 2023 18:54:12 +0000
parents 169b08c9713c
children
comparison
equal deleted inserted replaced
1:9c43baa60906 2:5fe20c915fa6
104 table_name, 104 table_name,
105 dict( 105 dict(
106 dbkey=index, 106 dbkey=index,
107 value='%s-%s' % (index, date.today().strftime("%d%m%Y")), 107 value='%s-%s' % (index, date.today().strftime("%d%m%Y")),
108 name="MetaPhlAn clade-specific marker genes (%s)" % index, 108 name="MetaPhlAn clade-specific marker genes (%s)" % index,
109 path=str(db_dp))) 109 path=str(db_dp),
110 db_version='SGB' if 'SGB' in index else 'legacy'))
110 111
111 112
112 if __name__ == "__main__": 113 if __name__ == "__main__":
113 print("Starting...") 114 print("Starting...")
114 115
127 print("Making %s" % target_dp) 128 print("Making %s" % target_dp)
128 target_dp.mkdir(parents=True, exist_ok=True) 129 target_dp.mkdir(parents=True, exist_ok=True)
129 130
130 # Set up data tables dictionary 131 # Set up data tables dictionary
131 data_tables = create_data_tables_dict() 132 data_tables = create_data_tables_dict()
132 add_data_table(data_tables, "metaphlan_database") 133 add_data_table(data_tables, "metaphlan_database_versioned")
133 134
134 # Fetch data from specified data sources 135 # Fetch data from specified data sources
135 print("Download and build database") 136 print("Download and build database")
136 download_metaphlan_db( 137 download_metaphlan_db(
137 data_tables, 138 data_tables,
138 args.index, 139 args.index,
139 "metaphlan_database", 140 "metaphlan_database_versioned",
140 target_dp) 141 target_dp)
141 142
142 # Write output JSON 143 # Write output JSON
143 print("Outputting JSON") 144 print("Outputting JSON")
144 with open(json_fp, 'w') as fh: 145 with open(json_fp, 'w') as fh: