Mercurial > repos > jjohnson > data_manager_snpeff

changeset 3:c6769a700e55

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Update loc data to separate version 4 databases
author Jim Johnson <jj@umn.edu>
date Tue, 21 Oct 2014 14:04:33 -0500
parents 5a01e5cfa6bc
children 6a378d0f4856
files data_manager/data_manager_snpEff_databases.py data_manager/data_manager_snpEff_download.py data_manager/data_manager_snpEff_download.xml data_manager_conf.xml tool-data/snpeff4_annotations.loc.sample tool-data/snpeff4_databases.loc.sample tool-data/snpeff4_genomedb.loc.sample tool-data/snpeff4_regulationdb.loc.sample tool-data/snpeff_annotations.loc.sample tool-data/snpeff_databases.loc.sample tool-data/snpeff_genomedb.loc.sample tool-data/snpeff_regulationdb.loc.sample tool_data_table_conf.xml.sample
diffstat 13 files changed, 43 insertions(+), 43 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_snpEff_databases.py	Mon Oct 20 13:17:12 2014 -0500
+++ b/data_manager/data_manager_snpEff_databases.py	Tue Oct 21 14:04:33 2014 -0500
@@ -37,7 +37,7 @@
     databases_output.close()
     try:
         data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
-        data_manager_dict['data_tables']['snpeff_databases'] = data_manager_dict['data_tables'].get( 'snpeff_databases', [] )
+        data_manager_dict['data_tables']['snpeff4_databases'] = data_manager_dict['data_tables'].get( 'snpeff4_databases', [] )
         data_table_entries = []
         fh = open(databases_path,'r')
         for i,line in enumerate(fh):
@@ -51,7 +51,7 @@
                     continue
                 description = fields[1].strip() + ' : ' + genome_version
                 data_table_entries.append(dict(value=genome_version, name=description))
-        data_manager_dict['data_tables']['snpeff_databases'] = data_table_entries
+        data_manager_dict['data_tables']['snpeff4_databases'] = data_table_entries
     except Exception, e:
         stop_err( 'Error parsing %s %s\n' % (config,str( e )) )
     else:
--- a/data_manager/data_manager_snpEff_download.py	Mon Oct 20 13:17:12 2014 -0500
+++ b/data_manager/data_manager_snpEff_download.py	Tue Oct 21 14:04:33 2014 -0500
@@ -110,18 +110,18 @@
                     # if snpEffectPredictor.bin download succeeded
                     name = genome_version + (' : ' + organism if organism else '') 
                     data_table_entry = dict(value=genome_version, name=name, path=data_dir)
-                    _add_data_table_entry( data_manager_dict, 'snpeff_genomedb', data_table_entry )
+                    _add_data_table_entry( data_manager_dict, 'snpeff4_genomedb', data_table_entry )
                 else:
                     m = re.match(regulation_pattern,fname)
                     if m:
                         name = m.groups()[0]
                         data_table_entry = dict(genome=genome_version,value=name, name=name)
-                        _add_data_table_entry( data_manager_dict, 'snpeff_regulationdb', data_table_entry )
+                        _add_data_table_entry( data_manager_dict, 'snpeff4_regulationdb', data_table_entry )
                     elif fname in annotations_dict:
                         value = annotations_dict[fname]
                         name = value.lstrip('-')
                         data_table_entry = dict(genome=genome_version,value=value, name=name)
-                        _add_data_table_entry( data_manager_dict, 'snpeff_annotations', data_table_entry )
+                        _add_data_table_entry( data_manager_dict, 'snpeff4_annotations', data_table_entry )
     return data_manager_dict
 
 def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ):
--- a/data_manager/data_manager_snpEff_download.xml	Mon Oct 20 13:17:12 2014 -0500
+++ b/data_manager/data_manager_snpEff_download.xml	Tue Oct 21 14:04:33 2014 -0500
@@ -28,7 +28,7 @@
             </when>
             <when value="cached">
                 <param name="genome_databases" type="select" display="checkboxes" multiple="true" label="Genome Version">
-                    <options from_data_table="snpeff_databases">
+                    <options from_data_table="snpeff4_databases">
                         <filter type="sort_by" column="0" />
                     </options>
                 </param>
@@ -46,13 +46,13 @@
     <tests>
         <test>
             <param name="genomeSrc"  value="named"/>
-            <param name="genome_version" value="GRCh37.71"/>
+            <param name="genome_version" value="GRCh38.76"/>
             <output name="out_file">
                 <assert_contents>
                     <!-- Check that a genome was added -->
-                    <has_text text="GRCh37.71" />
-                    <has_text text="snpeff_regulationdb" />
-                    <has_text text="snpeff_annotations" />
+                    <has_text text="GRCh38.76" />
+                    <has_text text="snpeff4_regulationdb" />
+                    <has_text text="snpeff4_annotations" />
                 </assert_contents>
             </output>
         </test>
--- a/data_manager_conf.xml	Mon Oct 20 13:17:12 2014 -0500
+++ b/data_manager_conf.xml	Tue Oct 21 14:04:33 2014 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <data_managers>
   <data_manager tool_file="data_manager/data_manager_snpEff_databases.xml" id="data_manager_snpeff_databases" >
-    <data_table name="snpeff_databases">  <!-- Defines a Data Table to be modified. -->
+    <data_table name="snpeff4_databases">  <!-- Defines a Data Table to be modified. -->
       <output> <!-- Handle the output of the Data Manager Tool -->
         <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
         <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool -->
@@ -9,27 +9,27 @@
     </data_table>
   </data_manager>
   <data_manager tool_file="data_manager/data_manager_snpEff_download.xml" id="data_manager_snpeff_download" >
-    <data_table name="snpeff_genomedb">  <!-- Defines a Data Table to be modified. -->
+    <data_table name="snpeff4_genomedb">  <!-- Defines a Data Table to be modified. -->
       <output> <!-- Handle the output of the Data Manager Tool -->
         <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
         <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
         <column name="path" output_ref="out_file" >
           <move type="directory" relativize_symlinks="True">
-            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">snpEff/data</target>
+            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">snpEff/v4/data</target>
           </move>
-          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/snpEff/data</value_translation>
+          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/snpEff/v4/data</value_translation>
           <value_translation type="function">abspath</value_translation>
         </column>
       </output>
     </data_table>
-    <data_table name="snpeff_regulationdb">  <!-- Defines a Data Table to be modified. -->
+    <data_table name="snpeff4_regulationdb">  <!-- Defines a Data Table to be modified. -->
       <output> <!-- Handle the output of the Data Manager Tool -->
         <column name="genome" /> <!-- columns that are going to be specified by the Data Manager Tool -->
         <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
         <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
       </output>
     </data_table>
-    <data_table name="snpeff_annotations">  <!-- Defines a Data Table to be modified. -->
+    <data_table name="snpeff4_annotations">  <!-- Defines a Data Table to be modified. -->
       <output> <!-- Handle the output of the Data Manager Tool -->
         <column name="genome" /> <!-- columns that are going to be specified by the Data Manager Tool -->
         <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/snpeff4_annotations.loc.sample	Tue Oct 21 14:04:33 2014 -0500
@@ -0,0 +1,5 @@
+## Regulation Databases for SnpEff 
+## These are from the list on: http://snpeff.sourceforge.net/download.html
+#genome	annotation_name description
+#GRCh37.71	nextprot	nextprot
+#GRCh37.71	motif	motif
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/snpeff4_databases.loc.sample	Tue Oct 21 14:04:33 2014 -0500
@@ -0,0 +1,5 @@
+## Available Databases for SnpEff 
+## These are from the list on: http://snpeff.sourceforge.net/download.html
+## the Description field in this sample is "Genome : Version" 
+#Version	Description
+#GRCh37.68	Homo sapiens : GRCh37.68
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/snpeff4_genomedb.loc.sample	Tue Oct 21 14:04:33 2014 -0500
@@ -0,0 +1,5 @@
+## Downloaded Databases for SnpEff 
+## These are from the list on: http://snpeff.sourceforge.net/download.html
+## the Description field in this sample is "Genome : Version" 
+#Version        Description	data_dir path
+#GRCh37.68      Homo sapiens : GRCh37.68	/home/galaxy/snpEff/data
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/snpeff4_regulationdb.loc.sample	Tue Oct 21 14:04:33 2014 -0500
@@ -0,0 +1,4 @@
+## Regulation Databases for SnpEff 
+## These are from the list on: http://snpeff.sourceforge.net/download.html
+#genome	regulation_name description
+#GRCh37.70	CD4	CD4
--- a/tool-data/snpeff_annotations.loc.sample	Mon Oct 20 13:17:12 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-## Regulation Databases for SnpEff 
-## These are from the list on: http://snpeff.sourceforge.net/download.html
-#genome	annotation_name description
-#GRCh37.71	nextprot	nextprot
-#GRCh37.71	motif	motif
--- a/tool-data/snpeff_databases.loc.sample	Mon Oct 20 13:17:12 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-## Available Databases for SnpEff 
-## These are from the list on: http://snpeff.sourceforge.net/download.html
-## the Description field in this sample is "Genome : Version" 
-#Version	Description
-#GRCh37.68	Homo sapiens : GRCh37.68
--- a/tool-data/snpeff_genomedb.loc.sample	Mon Oct 20 13:17:12 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-## Downloaded Databases for SnpEff 
-## These are from the list on: http://snpeff.sourceforge.net/download.html
-## the Description field in this sample is "Genome : Version" 
-#Version        Description	data_dir path
-#GRCh37.68      Homo sapiens : GRCh37.68	/home/galaxy/snpEff/data
--- a/tool-data/snpeff_regulationdb.loc.sample	Mon Oct 20 13:17:12 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-## Regulation Databases for SnpEff 
-## These are from the list on: http://snpeff.sourceforge.net/download.html
-#genome	regulation_name description
-#GRCh37.70	CD4	CD4
--- a/tool_data_table_conf.xml.sample	Mon Oct 20 13:17:12 2014 -0500
+++ b/tool_data_table_conf.xml.sample	Tue Oct 21 14:04:33 2014 -0500
@@ -1,19 +1,19 @@
 <tables>
-    <table name="snpeff_databases" comment_char="#">
+    <table name="snpeff4_databases" comment_char="#">
         <columns>value, name</columns>
-        <file path="tool-data/snpeff_databases.loc" />
+        <file path="tool-data/snpeff4_databases.loc" />
     </table>
-    <table name="snpeff_genomedb" comment_char="#">
+    <table name="snpeff4_genomedb" comment_char="#">
         <columns>value, name, path</columns>
-        <file path="tool-data/snpeff_genomedb.loc" />
+        <file path="tool-data/snpeff4_genomedb.loc" />
     </table>
-    <table name="snpeff_regulationdb" comment_char="#">
+    <table name="snpeff4_regulationdb" comment_char="#">
         <columns>genome, value, name</columns>
-        <file path="tool-data/snpeff_regulationdb.loc" />
+        <file path="tool-data/snpeff4_regulationdb.loc" />
     </table>
-    <table name="snpeff_annotations" comment_char="#">
+    <table name="snpeff4_annotations" comment_char="#">
         <columns>genome, value, name</columns>
-        <file path="tool-data/snpeff_annotations.loc" />
+        <file path="tool-data/snpeff4_annotations.loc" />
     </table>
 </tables>