Adding the GFF Loader code

tripal_core/gff_loader.php

@@ -0,0 +1,66 @@
+<?php
+
+function tripal_core_load_gff3() {
+   
+   $gff_file = drupal_get_path('module', 'tripal_core').'/test.gff3';
+
+   $lines = file($gff_file,FILE_SKIP_EMPTY_LINES);
+   $i = 0;
+
+   // get the controlled vocaubulary that we'll be using.  The
+   // default is the 'sequence' ontology
+   $vocab = 'sequence';
+   $sql = "SELECT * FROM cv WHERE name = '%s'";
+   $cv = db_fetch_object(db_query($sql,$vocab));
+
+   foreach ($lines as $line_num => $line) {
+      $i++;
+      $cols = explode("\t",$line);
+      if(sizeof($cols) > 9){
+         print "ERROR: improper number of columns on line $i\n";
+         return '';
+      }
+      // get the column values
+      $seqid = $cols[0];
+      $source = $cols[1];
+      $type = $cols[2];
+      $start = $cols[3];    
+      $end = $cols[4];
+      $score = $cols[5];
+      $strand = $cols[6];
+      $phase = $cols[7];
+      $attrs = explode(";",$cols[8]);  // split by a semi-colon
+      
+      // break apart each of the attributes
+      $tags = array();
+      foreach($attrs as $attr){
+         $attr = rtrim($attr);
+         $attr = ltrim($attr);
+         if(strcmp($attr,'')==0){
+            continue;
+         }
+         if(!preg_match('/^[^\=]+\=[^\=]+$/',$attr)){
+            print "ERROR: attribute is not correctly formatted on line $i: $attr\n";
+            return '';
+         }
+
+         // break apart each tag
+         $tag = explode("=",$attr);  // split by equals sign
+         // multiple instances of an attribute are separated by commas
+         $tags[$tag[0]] = explode(",",$tag[1]);  // split by comma
+      }
+
+      // remove URL encoding
+
+      // add the feature
+      $sql = "INSERT INTO {feature} (organism_id, name, uniquename, residues, seqlen,".
+             "    is_obsolete, type_id)".
+             " VALUES(%d,'%s','%s','%s',%d, %s, ".
+             "   (SELECT cvterm_id ".
+             "    FROM {CVTerm} CVT ".
+             "    INNER JOIN CV ON CVT.cv_id = CV.cv_id ".
+             "    WHERE CV.name = 'sequence' and CVT.name = '%s'))";
+
+   }
+   return '';
+}