diff data_manager/FROGS_data_manager.py @ 0:7caea40b2a30 draft

planemo upload commit c3ff1475af0e964a0c61458b66e2744c903d8d3d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/FROGS_data_manager.py	Wed Oct 02 11:00:08 2019 -0400
@@ -0,0 +1,87 @@
+# -*- coding: utf-8 -*-
+from galaxy.util.json import from_json_string, to_json_string
+import os, sys, argparse, time, json, requests, urllib
+
+def get_args():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-d","--database")
+    parser.add_argument("-r","--resource")
+    parser.add_argument("-o","--output")
+    args = parser.parse_args()
+    return args
+
+def _add_data_table_entry(data_manager_dict, data_table_entry,data_table):
+    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
+    data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get(data_table, [])
+    data_manager_dict['data_tables'][data_table].append(data_table_entry)
+    return data_manager_dict
+
+def frogs_sources(data_manager_dict,target_directory):
+
+    #get frogs database index
+    frogs_db_index_link="http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/FROGS_databases.tsv"
+    with requests.Session() as s:
+        download = s.get(frogs_db_index_link)
+        decoded_content = download.content.decode('utf-8')
+        db_index = download.content.splitlines()    
+        db_index = [line.split("\t") for line in db_index[1:]]
+        db_index = [line[:4]+[line[1]+"_"+line[2]+"_"+line[1]]+[line[4]] for line in db_index]  #add column name
+    
+    #get frogs dbs
+    dir_name="frogs_db_"+time.strftime("%Y%m%d")
+    os.mkdir(dir_name)
+    dbs=set([])
+    for line in db_index[:2]:
+        value=line[4]
+        name=value.replace("_"," ")
+        link=line[5]
+
+        #download frogs db
+        dl_file = urllib.URLopener()
+        dl_file.retrieve(link, "tmp.tar.gz")
+        
+        #unzip frogs db
+        with tarfile.open("tmp.tar.gz") as tar:
+            tar.extractall(dir_name)
+            tar.close()
+            os.remove('tmp.tar.gz')
+        
+        #get fasta file path
+        tmp = set(os.listdir(dir_name))
+        new_db = dir_name+"/"+"".join(tmp.difference(dbs))
+        files = os.listdir(new_db)
+        fasta = "".join([file for file in files if file.endswith('.fasta')])
+        path = new_db+'/'+fasta
+        dbs = os.listdir(dir_name)
+        release = value+"_"+time.strftime("%Y-%m-%d")
+        date=time.strftime("%Y%m%d")
+        path = os.path.join(target_directory,path)
+
+        data_table_entry = dict(name = name, value = value, path=path)
+        _add_data_table_entry(data_manager_dict, data_table_entry, "frogs_db")
+
+#def HVL_sources(resource):
+
+#def phiX_sources(resource):
+
+def main():
+
+    #get args from command line
+    args = get_args()
+
+    # Extract json file params
+    data_manager_dict = {}
+    filename = args.output
+    params = from_json_string(open(filename).read())
+    target_directory = params[ 'output_data' ][0]['extra_files_path']
+    os.mkdir(target_directory)
+
+    if args.database=="frogs_db_data":
+        frogs_sources(data_manager_dict,target_directory)
+    elif args.database=="HVL_db_data":
+        HVL_sources(args.resource)
+    elif args.database=="phiX_db_data":
+        phiX_sources(args.resource)
+
+if __name__ == "__main__":
+    main()