upload begin

blast_db.sh

+#!/bin/bash
+
+TOOL_DIR=$1
+TOOL_FILE=$2
+
+
+cd $TOOL_DIR
+makeblastdb -dbtype prot -in $TOOL_FILE
+rm $TOOL_FILE
+cd -
\ No newline at end of file

ghostx_db.sh

+#!/bin/bash
+
+TOOL_DIR=$1
+TOOL_FILE=$2
+cd $TOOL_DIR
+ghostx db -i $TOOL_FILE -o ghostx_db
+rm $TOOL_FILE
+cd -
\ No newline at end of file

ghostx_swissprot.sh

-#!/bin/bash
-
-DOWNLOAD_DIR=$1
-cd $DOWNLOAD_DIR
-ghostx db -i uniprot_sprot.fasta -o sp_ghost
-tar -czf sp_gx.tar.gz sp_ghost*
-rm uniprot_sprot*
-rm sp_ghost*
-cd -
\ No newline at end of file

main.py

-#!/home/theia/conda/bin/python
-import argparse
-import subprocess
-import os
-
-
-data = {'swissprot': {'prepare': './prepare_swissprot.sh',
-                    'tool': {'blast': './blast_swissprot.sh', 'ghostx': './ghostx_swissprot.sh'},
-                    'filename': 'uniprot_sprot.fasta'
-                    },
-            'pfam': {'prepare': './prepare_pfam.sh',
-                    'tool': {'hmmer': './hmmer_pfam.sh'},
-                    'filename': 'Pfam-A.hmm'
-                    },
-            'card': {
-                    }
-    }
-
-
-def myparser():
-    parser = argparse.ArgumentParser(description='Download, convert and share the data to working computer', prog='PSOT_database_maker')
-    
-    subparsers = parser.add_subparsers(title='Subcommands', description='Authorized Subcommands', help='Additional help')
-
-    prepare_parser = subparsers.add_parser('prepare', help='Databank download from the Website, extraction and transformation for another Programm')
-    prepare_parser.add_argument('database', help='Database which have to be prepared', type=str)
-    prepare_parser.add_argument('tool',help='Programm/Tool for the post analysis',type=str,)
-    prepare_parser.add_argument('-d', '--directory', dest='dir', help='target directory for the output.Default will be a created("output") folder in the working directory', type=str)
-    prepare_parser.set_defaults(func=prepare)
-
-    upload_parser = subparsers.add_parser('upload', help='Databank copy from the local directory to the web storage')
-    upload_parser.add_argument('file', help='File to be transfered from the local directory', type=str)
-    upload_parser.add_argument('-d', '--directory', dest='dir', help='Target directory for the file transfer into "S3". Default will be "s3://db_storage"', type=str)
-    upload_parser.set_defaults(func=upload)
-
-    download_parser = subparsers.add_parser('download', help='Datenbank copy from the web storage to the working computer')
-    download_parser.add_argument('file', help='File to be transfered from "S3"', type=str)
-    download_parser.add_argument('-d', '--directory', dest='dir', help='Target directory for the file transfer. Default will be a created folder("output) in the current working directory',type=str)
-    download_parser.set_defaults(func=download)
-
-    delete_parser = subparsers.add_parser('delete', help='delete existing files from local directory or from "S3"')
-    delete_parser.add_argument('database', help = 'database which have to be delete')
-    delete_parser.add_argument('place', choices = ['local','S3'], help = 'defined the place where the database have to be delete')
-    delete_parser.add_argument('-d', '--directory', dest='dir', help='directory where the database have to be delete')
-    delete_parser.set_defaults(func=delete)
-    return parser.parse_args()
-
-
-def targetdir_maker(args):
-    databasedir = "./output"
-    if args.dir:
-        databasedir = args.output
-    elif "dbman_dbdir" in os.environ:
-        databasedir = os.environ["dbman_dbdir"]
-    return databasedir
-
-# paste the target directory with the filename.(will be important to test if the file is already there. "/" or not)
-
-
-def filedir_maker(directory, file):
-    filedir = ''
-    if directory[-1] == '/':
-        filedir = directory+file
-    else:
-        filedir = directory+'/'+file
-    return filedir
-
-
-def prepare(args):
-    dbman_dir = targetdir_maker(args)
-    testfile = filedir_maker(dbman_dir, data[args.database]['filename'])
-    print(testfile)
-    if not os.path.isfile(testfile):
-        subprocess.run([data[args.database]['prepare'], dbman_dir])
-        subprocess.run([data[args.database]['tool'][args.tool], dbman_dir])
-        print("The {} file is in: ".format(args.database) + dbman_dir)
-    else:
-        print('The {} file already exists in :'.format(args.database) + dbman_dir)
-
-
-def upload(args):
-    dbman_dir = targetdir_maker(args)
-    subprocess.run(['./upload_db.sh', args.file, dbman_dir])
-
-
-def download(args):
-    dbman_dir = targetdir_maker(args)
-    subprocess.run(['./download_db.sh', args.file,dbman_dir])
-
-
-def delete(args):
-    if args.place == 'local':
-
-        dbman_dir = targetdir_maker(args)
-        testfile = filedir_maker(dbman_dir, data[args.database]['filename'])
-        if os.path.isfile(testfile):
-            subprocess.run(['./delete_db.sh',data[args.database]['filename'],dbman_dir])
-            print("The {} files were successfully delete in: ".format(args.database) + dbman_dir)
-        else:
-            print("The {} files aren't existing in: ".format(args.database) + dbman_dir)
-    else:
-        print('Skript für S3 noch nicht fertig')
-    
-def main():
-    if not os.path.isdir('output'):
-        os.mkdir('output')  
-
-    args=myparser()
-    args.func(args)
-
-
-if __name__=='__main__':
+#!/home/theia/conda/bin/python
+import argparse
+import subprocess
+import os
+import shutil
+
+data = {'swissprot': {'prepare': './prepare_swissprot.sh',
+                    'tool': {'blast': './blast_db.sh', 'ghostx': './ghostx_db.sh'},
+                    'filename':'uniprot_sprot.fasta'
+                    },
+            'pfam': {'prepare': './prepare_pfam.sh',
+                    'tool': {'hmmer': './hmmer_pfam.sh'},
+                    'filename':''
+                    },
+            'card': {'prepare':'./prepare_card.sh',
+                    'tool':{'blast':'./blast_db.sh','ghostx':'./ghostx_db.sh'},
+                    'filename':'protein_fasta_protein_homolog_model.fasta'
+                    }
+    }
+
+
+def myparser():
+    parser = argparse.ArgumentParser(description='Download, convert and share the data to working computer', prog='PSOT_database_maker')
+
+    subparsers = parser.add_subparsers(title='Subcommands', description='Authorized Subcommands', help='Additional help')
+
+    prepare_parser = subparsers.add_parser('prepare', help='Databank download from the Website, extraction and transformation for another Programm')
+    prepare_parser.add_argument('database', help='Database which have to be prepared', type=str)
+    prepare_parser.add_argument('tool',help='Programm/Tool for the post analysis',type=str,)
+    prepare_parser.add_argument('-d', '--directory', dest='dir', help='target directory for the output.Default will be a created("output") folder in the working directory', type=str)
+    prepare_parser.set_defaults(func=prepare)
+
+    upload_parser = subparsers.add_parser('upload', help='Databank copy from the local directory to the web storage')
+    upload_parser.add_argument('database', help='database to be transfered from the local directory', type=str)
+    upload_parser.add_argument('tool',type=str,help='database type which have to be transfered')
+    upload_parser.add_argument('-d', '--directory', dest='dir', help='Target directory for the file transfer into "S3". Default will be "s3://db_storage"', type=str)
+    upload_parser.set_defaults(func=upload)
+
+    download_parser = subparsers.add_parser('download', help='Datenbank copy from the web storage to the working computer')
+    download_parser.add_argument('file', help='File to be transfered from "S3"', type=str)
+    download_parser.add_argument('-d', '--directory', dest='dir', help='Target directory for the file transfer. Default will be a created folder("output) in the current working directory',type=str)
+    download_parser.set_defaults(func=download)
+
+    delete_parser = subparsers.add_parser('delete', help='delete existing files from local directory or from "S3"')
+    delete_parser.add_argument('database', help = 'database which have to be delete')
+    delete_parser.add_argument('place', choices = ['local','S3'], help = 'defined the place where the database have to be delete')
+    delete_parser.add_argument('-d', '--directory', dest='dir', help='directory where the database have to be delete')
+    delete_parser.set_defaults(func=delete)
+    return parser.parse_args()
+
+
+def targetdir_maker(args):
+    databasedir = "./output"
+    if args.dir:
+        databasedir = args.dir
+    elif "DBMAN_DBDIR" in os.environ:
+        databasedir = os.environ["DBMAN_DBDIR"]
+    return databasedir
+
+
+def s3dir_maker(args):
+    web_dir='s3://db_storage'
+    if args.dir:
+        web_dir=args.dir
+    elif 'S3_DBDIR' in os.environ:
+        web_dir=os.environ['S3_DBDIR']
+    return web_dir
+# paste the target directory with the filename.(will be important to test if the file is already there. "/" or not)
+
+
+def path_maker(directory, file):
+    filedir = ''
+    if directory[-1] == '/':
+        filedir = directory+file
+    else:
+        filedir = directory+'/'+file
+    return filedir
+
+
+def prepare(args):
+    if args.database in data.keys():
+
+        dbman_dir = targetdir_maker(args)
+        os.environ['PREPARE_DATA'] = dbman_dir
+        raw_dir = path_maker(dbman_dir, args.database+'_raw')
+
+        if not os.path.isdir(raw_dir):
+            os.mkdir(raw_dir)
+            subprocess.run([data[args.database]['prepare'], raw_dir])
+            print("The {} file is in: ".format(args.database) + raw_dir)
+        else:
+            print('The {} file already exists in: '.format(args.database) + raw_dir)
+        if args.tool in data[args.database]['tool'].keys():
+
+            tool_dir=path_maker(dbman_dir,args.database+'_'+args.tool)
+            tool_file=path_maker(raw_dir,data[args.database]['filename'])
+            if not os.path.isdir(tool_dir):
+                os.mkdir(tool_dir)
+                shutil.copy(tool_file,tool_dir)
+                subprocess.run([data[args.database]['tool'][args.tool], tool_dir, data[args.database]['filename']])
+                print('The {} files are in: '.format(args.tool) + tool_dir)
+        
+            else:
+                print('The {} files are already exists in: '.format(args.tool) + tool_dir)
+        else:
+            print('Tool error. Verify your input(tool) or/and check the possibility in the help')
+    else:
+        print('Database error. Verify your input(database) or/and check the possibility in the help')
+    return os.environ['PREPARE_DATA']
+
+
+def upload(args):
+    if args.database in data.keys() and args.tool in data[args.database]['tool'].keys():
+        dbman_dir = s3dir_maker(args)
+        dbdata = os.environ['PREPARE_DATA']
+        upload_data = args.database+'_'+args.tool
+        upload_data_path = path_maker(dbdata, upload_data)
+        upload_data_name = '{}'.format(upload_data+'.tar.gz')
+        if os.path.isdir(upload_data_path):
+            subprocess.run(['./upload_db.sh', dbdata, upload_data, dbman_dir, upload_data_name])
+        else:
+            print('There is no data for upload in {}. Prepare the database first'.format(dbdata))
+    else:
+        print('Verify your database and/or Tool input ')
+
+def download(args):
+    dbman_dir = targetdir_maker(args)
+    subprocess.run(['./download_db.sh', args.file,dbman_dir])
+
+
+def delete(args):
+    if args.place == 'local':
+
+        dbman_dir = targetdir_maker(args)
+        testfile = filedir_maker(dbman_dir, data[args.database]['filename'])
+        if os.path.isfile(testfile):
+            subprocess.run(['./delete_db.sh',data[args.database]['filename'],dbman_dir])
+            print("The {} files were successfully delete in: ".format(args.database) + dbman_dir)
+        else:
+            
+            print("The {} files aren't existing in: ".format(args.database) + dbman_dir)
+    else:
+        print('Skript für S3 noch nicht fertig')
+    
+def main():
+    if not os.path.isdir('output'):
+        os.mkdir('output')  
+
+    args=myparser()
+    args.func(args)
+
+
+if __name__=='__main__':
     main()
\ No newline at end of file

blast_swissprot.sh → prepare_card.sh

 #!/bin/bash
-
 DOWNLOAD_DIR=$1
 
 cd $DOWNLOAD_DIR
-makeblastdb -dbtype prot -in uniprot_sprot.fasta
-tar -czf sp_blast.tar.gz uniprot_sprot.*
+wget https://card.mcmaster.ca/download/0/broadstreet-v3.0.3.tar.gz
+tar xjf broadstreet-v3.0.3.tar.gz
 cd -
\ No newline at end of file

testfile.txt

@@ -87,3 +87,9 @@ default='s3://db_storage'
 
 
 ordner mit entsprechende namen!!!!
+
+Database repository---> https://github.com/MGX-metagenomics/databases/blob/master/card.build 
+
+anzeigen lassen---> echo $VARIABLE
+löschen---> unset VARIABLE
+setzen---> export VARIABLE = pfad
\ No newline at end of file

upload_db.sh

 #!/bin/bash
-Target_file=$1
-Target_dir=$2
-
-s3cmd put $Target_file $Target_dir
+DATA_DB=$1
+TARGET_FILE=$2
+TARGET_DIR=$3
+TARGET_FILE_NAME=$4
+cd $DATA_DB
+tar -czvf $TARGET_FILE_NAME $TARGET_FILE
+s3cmd put $TARGET_FILE_NAME $TARGET_DIR
+rm $TARGET_FILE_NAME
+cd -
\ No newline at end of file