erange version 4.0a dev release

[erange.git] / ReadDataset.py

diff --git a/ReadDataset.py b/ReadDataset.py
index ef80d657c721c837cbbc6c64d2a007d0fc6aa6e5..5ff60e2e6954c862888c5807495ef49142e14fa3 100644 (file)
--- a/ReadDataset.py
+++ b/ReadDataset.py
@@ -1,25 +1,12 @@
-"""
-Created on Jul 1, 2010
-
-@author: sau
-"""
-
 import sqlite3 as sqlite
 import string
 import tempfile
 import shutil
 import os
-from os import environ
 from array import array
-from commoncode import getReverseComplement
-
-if environ.get("CISTEMATIC_TEMP"):
-    cisTemp = environ.get("CISTEMATIC_TEMP")
-else:
-    cisTemp = "/tmp"
+from commoncode import getReverseComplement, getConfigParser, getConfigOption
 
-tempfile.tempdir = cisTemp
-currentRDSVersion = "1.1"
+currentRDSVersion = "2.0"
 
 
 class ReadDatasetError(Exception):
@@ -140,6 +127,9 @@ class ReadDataset():
     def cacheDB(self, filename):
         """ copy geneinfoDB to a local cache.
         """
+        configParser = getConfigParser()
+        cisTemp = getConfigOption(configParser, "general", "cistematic_temp", default="/tmp")
+        tempfile.tempdir = cisTemp
         self.cachedDBFile =  "%s.db" % tempfile.mktemp()
         shutil.copyfile(filename, self.cachedDBFile)
 
@@ -385,6 +375,8 @@ class ReadDataset():
         and which can be restricted by chromosome or custom-flag.
         Returns unique reads by default, but can return multireads
         with doMulti set to True.
+        
+        Need to rethink original design 1: Cannot have pairID without exporting as a readIDDict
         """
         whereClause = []
         resultsDict = {}