squash newlines in xml, change column heading to bionotate_xml

madprime · Jul 8, 2012 · 557aebb · 557aebb
1 parent db92b38
commit 557aebb
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/export_bionotate.php b/export_bionotate.php
@@ -1,6 +1,5 @@
 #!/usr/bin/php
-<?php
-    ;
+<?php ; // -*- mode: java; c-basic-indent: 4; tab-width: 4; indent-tabs-mode: nil; -*-
 
 chdir ('public_html');
 require_once 'lib/setup.php';
@@ -18,14 +17,15 @@
 ");
 if (theDb()->isError($q)) die ($q->getMessage() . "\n");
 
-$fields = split(' ', 'edit_timestamp edit_oid variant_id variant_gene variant_aa_del variant_aa_pos variant_aa_ins variant_rsid summary_long');
+$fields = split(' ', 'edit_timestamp edit_oid variant_id variant_gene variant_aa_del variant_aa_pos variant_aa_ins variant_rsid bionotate_xml');
 fputcsv($fh, $fields);
 
 $n=0;
 while ($row =& $q->fetchRow()) {
     $out = array();
+    $row['bionotate_xml'] = preg_replace('{\n}', '', $row['summary_long']);
     foreach ($fields as $f) {
-	$out[] = $row[$f];
+        $out[] = $row[$f];
     }
     fputcsv($fh, $out);
 }