diff data_manager/data_manager_humann2_download.py @ 0:048593e41359 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_humann2_download.py	Sun Mar 12 14:33:34 2017 -0400
@@ -0,0 +1,177 @@
+#!/usr/bin/env python
+#
+# Data manager for reference data for the 'humann2' Galaxy tools
+import datetime
+import json
+import optparse
+import os
+import subprocess
+import sys
+
+
+HUMANN2_REFERENCE_DATA = {
+    "full": "Full",
+    "DEMO": "Demo",
+    "uniref50_diamond": "Full UniRef50",
+    "uniref50_ec_filtered_diamond": "EC-filtered UniRef50",
+    "uniref50_GO_filtered_rapsearch2": "GO filtered UniRef50 for rapsearch2",
+    "uniref90_diamond": "Full UniRef50",
+    "uniref90_ec_filtered_diamond": "EC-filtered UniRef90",
+    "DEMO_diamond": "Demo"
+}
+
+
+# Utility functions for interacting with Galaxy JSON
+def read_input_json(jsonfile):
+    """Read the JSON supplied from the data manager tool
+
+    Returns a tuple (param_dict,extra_files_path)
+
+    'param_dict' is an arbitrary dictionary of parameters
+    input into the tool; 'extra_files_path' is the path
+    to a directory where output files must be put for the
+    receiving data manager to pick them up.
+
+    NB the directory pointed to by 'extra_files_path'
+    doesn't exist initially, it is the job of the script
+    to create it if necessary.
+
+    """
+    params = json.loads(open(jsonfile).read())
+    return (params['param_dict'],
+            params['output_data'][0]['extra_files_path'])
+
+
+# Utility functions for creating data table dictionaries
+#
+# Example usage:
+# >>> d = create_data_tables_dict()
+# >>> add_data_table(d,'my_data')
+# >>> add_data_table_entry(dict(dbkey='hg19',value='human'))
+# >>> add_data_table_entry(dict(dbkey='mm9',value='mouse'))
+# >>> print str(json.dumps(d))
+def create_data_tables_dict():
+    """Return a dictionary for storing data table information
+
+    Returns a dictionary that can be used with 'add_data_table'
+    and 'add_data_table_entry' to store information about a
+    data table. It can be converted to JSON to be sent back to
+    the data manager.
+
+    """
+    d = {}
+    d['data_tables'] = {}
+    return d
+
+
+def add_data_table(d, table):
+    """Add a data table to the data tables dictionary
+
+    Creates a placeholder for a data table called 'table'.
+
+    """
+    d['data_tables'][table] = []
+
+
+def add_data_table_entry(d, table, entry):
+    """Add an entry to a data table
+
+    Appends an entry to the data table 'table'. 'entry'
+    should be a dictionary where the keys are the names of
+    columns in the data table.
+
+    Raises an exception if the named data table doesn't
+    exist.
+
+    """
+    try:
+        d['data_tables'][table].append(entry)
+    except KeyError:
+        raise Exception("add_data_table_entry: no table '%s'" % table)
+
+
+def download_humann2_db(data_tables, table_name, database, build, target_dir):
+    """Download HUMAnN2 database
+
+    Creates references to the specified file(s) on the Galaxy
+    server in the appropriate data table (determined from the
+    file extension).
+
+    The 'data_tables' dictionary should have been created using
+    the 'create_data_tables_dict' and 'add_data_table' functions.
+
+    Arguments:
+      data_tables: a dictionary containing the data table info
+      table_name: name of the table
+      database: database to download (chocophlan or uniref)
+      build: build of the database to download
+      target_dir: directory to put copy or link to the data file
+
+    """
+    value = "%s-%s-%s" % (database, build, datetime.date.today().isoformat())
+    db_target_dir = os.path.join(target_dir, database)
+    build_target_dir = os.path.join(db_target_dir, build)
+    os.makedirs(build_target_dir)
+    cmd = "humann2_databases --download %s %s %s" % (database,
+                                                     build,
+                                                     db_target_dir)
+    subprocess.check_call(cmd, shell=True)
+    print(os.listdir(db_target_dir))
+    os.rename(os.path.join(db_target_dir, database), build_target_dir)
+    print(os.listdir(db_target_dir))
+    add_data_table_entry(
+        data_tables,
+        table_name,
+        dict(
+            dbkey=build,
+            value=value,
+            name=HUMANN2_REFERENCE_DATA[build],
+            path=build_target_dir))
+
+
+if __name__ == "__main__":
+    print("Starting...")
+
+    # Read command line
+    parser = optparse.OptionParser(description='Download HUMAnN2 database')
+    parser.add_option('--database', help="Database name")
+    parser.add_option('--build', help="Build of the database")
+    options, args = parser.parse_args()
+    print("args   : %s" % args)
+
+    # Check for JSON file
+    if len(args) != 1:
+        sys.stderr.write("Need to supply JSON file name")
+        sys.exit(1)
+
+    jsonfile = args[0]
+
+    # Read the input JSON
+    params, target_dir = read_input_json(jsonfile)
+
+    # Make the target directory
+    print("Making %s" % target_dir)
+    os.mkdir(target_dir)
+
+    # Set up data tables dictionary
+    data_tables = create_data_tables_dict()
+
+    if options.database == "chocophlan":
+        table_name = 'humann2_nucleotide_database'
+    else:
+        table_name = 'humann2_protein_database'
+    add_data_table(data_tables, table_name)
+
+    # Fetch data from specified data sources
+    download_humann2_db(
+        data_tables,
+        table_name,
+        options.database,
+        options.build,
+        target_dir)
+
+    # Write output JSON
+    print("Outputting JSON")
+    print(str(json.dumps(data_tables)))
+    open(jsonfile, 'wb').write(json.dumps(data_tables))
+    print("Done.")