fix loading of GO-assoc, string-db update version

patflick · Feb 15, 2016 · 233f831 · 233f831
1 parent d376c33
commit 233f831
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/data/download_data.sh b/data/download_data.sh
@@ -44,7 +44,7 @@ cp $TMP_FOLDER/CRG-human-interactome/CRG.integrated.human.interactome.txt ppis/
 # an account to download)
 
 # 3.) string-db
-STRING_VERSION=9.05
+STRING_VERSION=10
 STRING_CUTOFF=500 # cutoff at a reliability of 700 for import
 STRING_URL=https://string-db.com/newstring_download/protein.links.v$STRING_VERSION.txt.gz
 STRING_GZ=$DOWNLOAD_FOLDER/protein.links.v$STRING_VERSION.txt.gz

diff --git a/src/pappi/go/import_ass.py b/src/pappi/go/import_ass.py
@@ -13,4 +13,4 @@ def import_go_association(filename, sql_conn, table=GO_ASSOC_TABLE):
  """
  sql.import_csv(filename, table, '\t', False, import_columns=[2, 4],
  column_names=["Gene", "GOTerm"], sql_conn=sql_conn,
- skip_rows=9)
+ skip_rows=12)