src/hg/near/hprdXmlToTab/out.atree 1.1

1.1 2009/10/15 21:58:38 kent
Utility to convert HPRD interaction html file to tab-separated list of protein/protein interactions seems to work. This is based on an autoXml parser and a snippet of code Galt wrote that now lives in hprdXmlToTab.c.
Index: src/hg/near/hprdXmlToTab/out.atree
===================================================================
RCS file: src/hg/near/hprdXmlToTab/out.atree
diff -N src/hg/near/hprdXmlToTab/out.atree
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/near/hprdXmlToTab/out.atree	15 Oct 2009 21:58:38 -0000	1.1
@@ -0,0 +1,71 @@
+entrySet #level #version $xmlns $xmlns:xsi $xsi:schemaLocation
+  entry
+    source
+      names
+        $shortLabel
+        $fullName?
+        $alias* $type $typeAc
+      bibref
+        xref
+          primaryRef $db $id $dbAc? $refType? $refTypeAc?
+          secondaryRef* $db $id $dbAc? $refType? $refTypeAc?
+    availabilityList
+      $availability #id
+    experimentList
+      experimentDescription* #id
+        bibref
+          xref
+            primaryRef $db $id $dbAc? $refType? $refTypeAc?
+            secondaryRef* $db $id $dbAc? $refType? $refTypeAc?
+        interactionDetectionMethod
+          names
+            $shortLabel
+            $fullName?
+            $alias* $type $typeAc
+          xref
+            primaryRef $db $id $dbAc? $refType? $refTypeAc?
+            secondaryRef* $db $id $dbAc? $refType? $refTypeAc?
+      #experimentRef*
+    interactorList
+      interactor+ $id
+        names
+          $shortLabel
+          $fullName?
+          $alias* $type $typeAc
+        xref
+          primaryRef $db $id $dbAc? $refType? $refTypeAc?
+          secondaryRef* $db $id $dbAc? $refType? $refTypeAc?
+        interactorType
+          names
+            $shortLabel
+            $fullName?
+            $alias* $type $typeAc
+          xref
+            primaryRef $db $id $dbAc? $refType? $refTypeAc?
+            secondaryRef* $db $id $dbAc? $refType? $refTypeAc?
+        organism #ncbiTaxId
+          names
+            $shortLabel
+            $fullName?
+            $alias* $type $typeAc
+        $sequence
+    interactionList
+      interaction+ #id
+        experimentList
+          experimentDescription* #id
+            bibref
+              xref
+                primaryRef $db $id $dbAc? $refType? $refTypeAc?
+                secondaryRef* $db $id $dbAc? $refType? $refTypeAc?
+            interactionDetectionMethod
+              names
+                $shortLabel
+                $fullName?
+                $alias* $type $typeAc
+              xref
+                primaryRef $db $id $dbAc? $refType? $refTypeAc?
+                secondaryRef* $db $id $dbAc? $refType? $refTypeAc?
+          #experimentRef*
+        participantList
+          participant+ #id
+            $interactorRef