[Obo-svn-commit] SF.net SVN: obo: [1787] obo-database/trunk/bin/obd-fix-omim-genotypes.pl

[<cmu...@us...>]

Revision: 1787
          http://obo.svn.sourceforge.net/obo/?rev=1787&view=rev
Author:   cmungall
Date:     2008-05-13 11:48:01 -0700 (Tue, 13 May 2008)

Log Message:
-----------


Added Paths:
-----------
    obo-database/trunk/bin/obd-fix-omim-genotypes.pl

Added: obo-database/trunk/bin/obd-fix-omim-genotypes.pl
===================================================================
--- obo-database/trunk/bin/obd-fix-omim-genotypes.pl	                        (rev 0)
+++ obo-database/trunk/bin/obd-fix-omim-genotypes.pl	2008-05-13 18:48:01 UTC (rev 1787)
@@ -0,0 +1,40 @@
+#!/usr/bin/perl -w
+
+use DBIx::DBStag;
+
+my $sdbh = DBIx::DBStag->connect(shift);
+
+my $dbh = $sdbh->dbh;
+
+my $rows = $dbh->selectall_arrayref("SELECT node_id,uid FROM node WHERE uid like 'OMIM:%'");
+
+foreach my $row (@$rows) {
+    my ($id,$uid) = @$row;
+    print STDERR "$uid\n";
+    my $ref;
+    my $gtnum;
+    if ($uid =~ /OMIM:(\d+)\.(\d+)/) {
+        $ref = "MIM:$1-$2";
+        $gtnum = $2;
+    }
+    elsif ($uid =~ /OMIM:(\d+)/) {
+        $ref = "MIM:$1";
+    }
+    if (!$gtnum) {
+        $gtnum = $uid;
+        $gtnum =~ s/OMIM://;
+        $gtnum =~ s/.*\.//;
+    }
+    my $refrows = $dbh->selectall_arrayref("SELECT node_id,uid FROM node WHERE uid = '$ref'");
+    foreach my $refrow (@$refrows) {
+        print STDERR "  @$refrow\n";
+        $dbh->do("SELECT store_node_dbxref_i($id,'$ref')");
+    }
+    my $generows = $dbh->selectall_arrayref("SELECT object_id,object_uid,object_label FROM node_link_node_with_pred WHERE node_uid = '$uid' and pred_uid='OBO_REL:variant_of'");
+    foreach my $grow (@$generows) {
+        my $label = sprintf("%s OMIM genotype %s",$grow->[2],"$gtnum");
+        print STDERR "  G:@$grow :: $label\n";
+        
+        $dbh->do("UPDATE node SET label = '$label' WHERE node_id=$id");
+    }
+}


Property changes on: obo-database/trunk/bin/obd-fix-omim-genotypes.pl
___________________________________________________________________
Name: svn:executable
   + *


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