From c41b730f7ccf9b8de4753e32db21cac2baec11d8 Mon Sep 17 00:00:00 2001
From: Kelly Vincent <kpvincent@bx.psu.edu>
Date: Thu, 1 Oct 2009 13:16:43 -0400
Subject: [PATCH] Updated BWA and Bowtie wrapper tools so that the dbkey of the
 output is correctly assigned

---
 tools/sr_mapping/bowtie_wrapper.xml     |  2 +-
 tools/sr_mapping/bowtie_wrapper_code.py | 15 +++++++++++++++
 tools/sr_mapping/bwa_wrapper.xml        |  2 --
 tools/sr_mapping/bwa_wrapper_code.py    |  7 +++++--
 4 files changed, 21 insertions(+), 5 deletions(-)
 create mode 100644 tools/sr_mapping/bowtie_wrapper_code.py

diff --git a/tools/sr_mapping/bowtie_wrapper.xml b/tools/sr_mapping/bowtie_wrapper.xml
index acbc1c7719e..f77c9973914 100644
--- a/tools/sr_mapping/bowtie_wrapper.xml
+++ b/tools/sr_mapping/bowtie_wrapper.xml
@@ -152,7 +152,6 @@
   	      <options from_file="bowtie_indices.loc">
   	        <column name="value" index="1" />
   	        <column name="name" index="0" />
-  	        <filter type="sort_by" column="0" />
   	      </options>
   	    </param>
   	  </when>
@@ -540,4 +539,5 @@ For aligning (bowtie)::
 	--seed &lt;int&gt;       Random seed. Use &lt;int&gt; as the seed for the pseudo-random number generator. [off]
 
   </help>
+  <code file="bowtie_wrapper_code.py" />
 </tool>
diff --git a/tools/sr_mapping/bowtie_wrapper_code.py b/tools/sr_mapping/bowtie_wrapper_code.py
new file mode 100644
index 00000000000..21a8f6b44eb
--- /dev/null
+++ b/tools/sr_mapping/bowtie_wrapper_code.py
@@ -0,0 +1,15 @@
+import os
+
+def exec_before_job(app, inp_data, out_data, param_dict, tool):
+    try:
+        refFile = param_dict['refGenomeSource']['indices'].value
+        dbkey = os.path.split(refFile)[1].split('.')[0]
+        # deal with the one odd case
+        if dbkey.find('chrM') >= 0:
+            dbkey = 'equCab2'
+        out_data['output'].set_dbkey(dbkey)
+    except:
+        try:
+            refFile = param_dict['refGenomeSource']['ownFile'].dbkey
+        except:
+            out_data['output'].set_dbkey('?')     
diff --git a/tools/sr_mapping/bwa_wrapper.xml b/tools/sr_mapping/bwa_wrapper.xml
index ccfb55bb26b..41fefbabd47 100644
--- a/tools/sr_mapping/bwa_wrapper.xml
+++ b/tools/sr_mapping/bwa_wrapper.xml
@@ -80,7 +80,6 @@
  	  	      <options from_file="sequence_index_color.loc">
   	  	        <column name="value" index="1" />
 	  	        <column name="name" index="0" />
-	  	        <filter type="sort_by" column="0" />
 	  	      </options>
 	  	    </param>
 	  	  </when>
@@ -100,7 +99,6 @@
  	  	      <options from_file="sequence_index_base.loc">
   	  	        <column name="value" index="1" />
 	  	        <column name="name" index="0" />
- 	  	        <filter type="sort_by" column="0" />
 	  	      </options>
 	        </param>
 	      </when>
diff --git a/tools/sr_mapping/bwa_wrapper_code.py b/tools/sr_mapping/bwa_wrapper_code.py
index a8e19e6bc77..cecaa528838 100644
--- a/tools/sr_mapping/bwa_wrapper_code.py
+++ b/tools/sr_mapping/bwa_wrapper_code.py
@@ -4,5 +4,8 @@ def exec_before_job(app, inp_data, out_data, param_dict, tool):
     try:
         refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['indices'].value
         out_data['output'].set_dbkey(os.path.split(refFile)[1].split('.')[0])
-    except Exception, eq:
-        out_data['output'].set_dbkey(param_dict['dbkey'])     
+    except:
+        try:
+            refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['ownFile'].dbkey
+        except:
+            out_data['output'].set_dbkey('?')