prepare

README.md

-# psotdb
-test3

Untitled.txt

+subcommands für argparse
+
+einzelne prameter zusammenbauen
+

blast_swissprot.sh

+#!/bin/bash
+
+DOWNLOAD_DIR=$1
+
+cd $DOWNLOAD_DIR
+makeblastdb -dbtype prot -in ../dbx/uniprot_sprot.fasta
+tar -czf sp_blast.tar.gz uniprot_sprot.*
+rm uniprot_sprot*
+cd -
\ No newline at end of file

download_pfam.sh

+#!/bin/bash
+DOWNLOAD_DIR=$1
+
+cd $DOWNLOAD_DIR
+wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.fasta.gz
+gunzip Pfam-A.fasta.gz
+cd -
\ No newline at end of file

download_swissprot.sh

+#!/bin/bash
+DOWNLOAD_DIR=$1
+
+cd $DOWNLOAD_DIR
+wget ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/uniprot_sprot.fasta.gz
+gunzip uniprot_sprot.fasta.gz
+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
+
+data={'swissprot':{'download':'./download_swissprot.sh','blast':'./blast_swissprot.sh','ghostx':'./ghostx_swissprot.sh'},'pfam':{'download':'./download_pfam.sh'}}
 parser=argparse.ArgumentParser(description='Vorbereitung von Datenbanken für PSOT(lädt Daten herunter, wandelt die um und stellt die Daten den Rechnern zur Verfügung)',prog='psotdb')
 parser.add_argument('-o','--option',dest='opt')
+parser.add_argument('-b','--bank',dest='bank')
+parser.add_argument('-t','--tool',dest='tool')
 args=parser.parse_args()
-print(args.opt)
+
+if args.opt.lower()=='prepare':
+    file=subprocess.run([data[args.bank]['download'],'../dbx'])
+    if args.tool:
+        file_tool=subprocess.run([data[args.bank][args.tool],'../dbx'])
+    
+elif args.opt.lower()=='upload':
+    print('hochladen')
+elif args.opt.lower()=='download':
+    print('herunterladen')
+else:
+    print('geht nicht')