From: Diane Trout <diane@caltech.edu>
Date: Wed, 18 Mar 2009 19:20:49 +0000 (+0000)
Subject: Generate a gerald config file, even if the genome is unknown
X-Git-Tag: 0.2.0.2~8
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=526a63bf0aef0e361fdccb65aedfa18b6f7bf1c0

Generate a gerald config file, even if the genome is unknown
as it makes it easier to edit the wrong config file and manually launch
an analysis.
---

diff --git a/htsworkflow/pipelines/genome_mapper.py b/htsworkflow/pipelines/genome_mapper.py
index a8ea871..d29e446 100644
--- a/htsworkflow/pipelines/genome_mapper.py
+++ b/htsworkflow/pipelines/genome_mapper.py
@@ -80,24 +80,28 @@ class constructMapperDict(object):
         Return the best match for key
         """
         elements = re.split("\|", key)
-          
-        if len(elements) == 1:
-            # we just the species name
-            # get the set of builds
-            builds = self.genome_dict[elements[0]]
+        
+        try:  
+            if len(elements) == 1:
+                # we just the species name
+                # get the set of builds
+                builds = self.genome_dict[elements[0]]
             
-            # sort build names the way humans would
-            keys = builds.keys()
-            keys.sort(cmp=alphanum)
+                # sort build names the way humans would
+                keys = builds.keys()
+                keys.sort(cmp=alphanum)
             
-            # return the path from the 'last' build name
-            return builds[keys[-1]]
+                # return the path from the 'last' build name
+                return builds[keys[-1]]
                         
-        elif len(elements) == 2:
-            # we have species, and build name
-            return self.genome_dict[elements[0]][elements[1]]
-        else:
-            raise KeyError("Unrecognized key")
+            elif len(elements) == 2:
+                # we have species, and build name
+                return self.genome_dict[elements[0]][elements[1]]
+            else:
+                raise KeyError("Unrecognized key")
+        except KeyError, e:
+            logging.error('Unrecognized genome identifier: %s' % str((elements),))
+            return "NoGenomeAvailable"
         
     def keys(self):
         keys = []