diff galaxy-tools/biobank/tools/map_vid.py @ 0:ba6cf6ede027 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/tools/map_vid.py	Wed Sep 28 06:03:30 2016 -0400
@@ -0,0 +1,25 @@
+# BEGIN_COPYRIGHT
+# END_COPYRIGHT
+
+import sys
+from bl.vl.app.kb_query.main import main as kb_query
+
+def main(argv):
+  selected_column, new_column_name, input_file = argv[:3]
+  selected_column = int(selected_column) - 1
+  new_column_name = new_column_name.strip()
+
+  # with open(input_file) as f:
+  #   l = f.readline().strip()
+  # Backport to 2.6
+  fi = open(input_file)
+  l = fi.readline().strip()
+  fi.close()
+
+  column_names = l.split('\t')
+  column_name = column_names[selected_column]
+
+  argv = argv[3:] + ['--column=%s,%s' % (column_name, new_column_name)]
+  kb_query(argv)
+
+main(sys.argv[1:])