allow annotation section in settings for backwards compatibility

-  issue warning instead of error
- propagete old annotation paths to locations dict

if paths are given, this still requires that annotation files exist and for old annotation specification does not allow relative paths

scripts/validate_config.py

@@ -20,7 +20,7 @@
 import os
 import csv
 from glob import glob
-from func_defs import bail
+from func_defs import bail, warn
 
 # ==============================================================================
 #
@@ -102,11 +102,29 @@ def parse_samples(lines):
     return { 'SAMPLES': outputdict }
 
 
+def update_config_layout(config):
+    # check for new annotation layout
+    if 'annotation' in config['general']['differential-methylation']:
+        warn("The specification of annotation files has changed in version 0.1.9 \n"+
+        "For now updating configuration file with the new default settings layout.\n"+
+        "In the future, please retrieve the new default settings layout with 'pigx-bsseq --init settings'.")
+
+    ## move cpgisland and refgene files to location dict
+    if 'cpgIsland-bedfile' in config['general']['differential-methylation']['annotation']:
+            config['locations']['cpgIsland-bedfile'] = config['general']['differential-methylation']['annotation']['cpgIsland-bedfile']
+    if 'refGenes-bedfile' in config['general']['differential-methylation']['annotation']:
+            config['locations']['refGenes-bedfile'] = config['general']['differential-methylation']['annotation']['refGenes-bedfile']
+
+    ## remove annotation section
+    config['general']['differential-methylation'].pop('annotation')
+
+    return config
+
+
+
 # --------------------------------------
 # validation of Config 
 # --------------------------------------
-
-
 # check for common input/configuration errors:
 def validate_config(config):
     # Check that all locations exist
@@ -150,10 +168,6 @@ def validate_config(config):
         "Please retrieve the new default settings layout with 'pigx-bsseq --init settings'.\n")
 
 
-    # check for new annotation layout
-    if 'annotation' in config['general']['differential-methylation']:
-        bail("ERROR: The specification of annotation files has changed.\n"+
-        "Please retrieve the new default settings layout with 'pigx-bsseq --init settings'.\n")