Add a test for the sample analysis of retrieving genes flanked by DNAse HSS.

2026-09-24 16:30:27 +08:00 · 2008-11-07 16:27:07 -05:00
parent 8ff58ac96f
commit b853633200
1 changed files with 79 additions and 0 deletions
@@ -0,0 +1,79 @@
+from base.twilltestcase import TwillTestCase
+
+""" A sample analysis"""
+
+
+
+class AnalysisDNAseHSSFlankedGenes( TwillTestCase ):
+    
+    def test_get_DNAseHSS_flanked_genes( self ):
+        self.login()
+        
+        self.new_history()
+    
+        track_params = dict(
+            db="hg17",
+            hgta_group="regulation",
+            hgta_table="dukeDnaseCd4Sites",
+            hgta_track="dukeDnaseCd4Sites",
+            hgta_regionType="range",
+            position="chr22",
+            hgta_outputType="bed",
+            sendToGalaxy="1"
+        )
+        output_params = dict(
+            fbQual="whole",
+        )
+        
+        self.run_ucsc_main( track_params, output_params )
+        self.wait()
+        self.verify_dataset_correctness('DNAseHSS.dat')
+        
+        self.edit_metadata( name="DNAse HS" )
+        self.check_metadata_for_string( "DNAse HS" )
+        
+        track_params = dict(
+            db="hg17",
+            hgta_group="genes",
+            hgta_table="knownGene",
+            hgta_track="knownGene",
+            hgta_regionType="range",
+            position="chr22",
+            hgta_outputType="bed",
+            sendToGalaxy="1"
+        )
+        output_params = dict(
+            fbQual="whole",
+        )
+        
+        self.run_ucsc_main( track_params, output_params )
+        self.wait()
+        self.verify_dataset_correctness('hg17chr22KnownGenes.dat')
+        
+        self.edit_metadata( name="Genes" )
+        self.check_metadata_for_string( "Genes" )
+        
+        
+        self.run_tool( 'get_flanks1', input="2", region="whole", direction="Upstream", offset="0", size="500" )
+        self.wait()
+        self.verify_dataset_correctness( 'knownGeneUpstream500Flanks.dat' )
+        
+        self.edit_metadata( name="Flanks" )
+        self.check_metadata_for_string( "Flanks" )
+        
+        
+        self.run_tool( 'gops_join_1', input1="3", input2="1", min="1", fill="none"  )
+        self.wait()
+        #self.verify_dataset_correctness( 'joinFlanksDNAse.dat' ) #we cannot verify this dataset, because this tool spits out data in a non-deterministic order
+        
+        
+        self.run_tool( 'Filter1', input="4", cond="c17==1000"  )
+        self.wait()
+        self.verify_dataset_correctness( 'filteredJoinedFlanksDNAse.dat' )
+        
+        
+        self.delete_history()
+        self.logout()
+        
+        
+