From: athreyab <athreyab@localhost>
Date: Tue, 31 Jan 2012 22:56:55 +0000 (+0000)
Subject: allow sif file to be a source of gene information
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=d170f6e8008585e97a112faf47531cda52c1fe7f;p=old-jaiswallab-svn%2F.git

allow sif file to be a source of gene information

svn path=/; revision=290
---

diff --git a/Personnel/athreyab/interactions/interactionPathsFromSif.pl b/Personnel/athreyab/interactions/interactionPathsFromSif.pl
index 9e5b5bb..eb93e75 100644
--- a/Personnel/athreyab/interactions/interactionPathsFromSif.pl
+++ b/Personnel/athreyab/interactions/interactionPathsFromSif.pl
@@ -165,25 +165,32 @@ sub importSifData
 		# strip off newline characters
 		chomp $entry;
 		$entry =~ s/\r//g;
-      $entry =~ s/\n//g;
-      
-      # split the columns into separate variables
-      my ($accession_left,$interaction_type,$accession_right) = split("\t", $entry);
-      
-      # skip if any of the variables are empty      
-      next if(isEmpty($accession_left));
+    $entry =~ s/\n//g;
+
+		# split the columns into separate variables
+    my ($accession_left,$interaction_type,$accession_right) = split("\t", $entry);
+    
+    # skip if any of the variables are empty      
+    next if(isEmpty($accession_left));
 		next if(isEmpty($interaction_type));
 		next if(isEmpty($accession_right));
       
-      #get object_id for object in the first column
+    #get object_id for object in the first column
 		$accession_left_id = getObjectIdFromAccession($accession_left);
-
-		#get interaction_type_id for object in the first column
-		$interaction_type_id = getInteractionTypeForSifFormat($interaction_type);
+		if(isEmpty($accession_left_id)){
+			$query = "INSERT INTO Object(`object_accession`, `species_id`) VALUES ('$accession_left', '$speciesIdForSif')";
+			executeDbQuery($query);		
+			$accession_left_id = getObjectIdFromAccession($accession_left);
+		}
 
 		#get object_id for object in the second column
 		$accession_right_id = getObjectIdFromAccession($accession_right);
-
+		if(isEmpty($accession_right_id)){
+			$query = "INSERT INTO Object(`object_accession`, `species_id`) VALUES ('$accession_right', '$speciesIdForSif')";
+			executeDbQuery($query);		
+			$accession_right_id = getObjectIdFromAccession($accession_right);
+		}
+		$interaction_type_id=getInteractionTypeForSifFormat($interaction_type);
 		next if(isEmpty($accession_left_id) || isEmpty($accession_right_id) || isEmpty($interaction_type_id));
 		
 		#check if the interaction is already recorded. Write to database only if it doesn't exist already.e