Mercurial > repos > eschen42 > mqppep_preproc

diff search_ppep.py @ 6:42daf70d4ed4 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
author eschen42
date Fri, 11 Mar 2022 20:04:40 +0000
parents b91809a18dbe
children ba5f14c2a4af
line wrap: on
line diff
--- a/search_ppep.py	Thu Mar 10 23:43:38 2022 +0000
+++ b/search_ppep.py	Fri Mar 11 20:04:40 2022 +0000
@@ -516,6 +516,16 @@
     for row in ker.fetchall():
         print(row[0])
 
+    # link peptides not found in sequence database to a dummy sequence-record
+    ker.execute(
+        """
+        INSERT INTO deppep_UniProtKB(deppep_id,UniProtKB_id,pos_start,pos_end)
+          SELECT id, 'No Uniprot_ID', 0, 0
+          FROM   deppep
+          WHERE  id NOT IN (SELECT deppep_id FROM deppep_UniProtKB)
+        """
+    )
+
     con.commit()
     ker.execute("vacuum")
     con.close()