reverted to multiloop and corrected counter bug

api/blast_ui.api.inc

@@ -712,7 +712,6 @@ function convert_tsv2gff3($blast_tsv,$blast_gff){
   $tsv = fopen($blast_tsv, "r") or die("Unable to open tsv file!");
 
   // For each line in the TSV file...
-  // Need to go thru each line of tsv to find the first and last hsp of a hit.
   $results = array();
   while(!feof($tsv)) {
     $line = fgets($tsv);
@@ -749,19 +748,20 @@ function convert_tsv2gff3($blast_tsv,$blast_gff){
     $hspInfo = "$queryId,$subjectStart,$subjectEnd,$queryStart,$queryEnd";
     $results[$hitname][$hspInfo] = $eval;
   } // end tsv file while
+
   $IDs = array();
   $count = 0;
   $last_s = NULL;
-   
-  // Need to get the smallest and largest coordinate for the parent feature
+
+    // Need to go thru each line of tsv to find the first and last hsp of a hit.
+    // Need to get the smallest and largest coordinate for the parent feature
     foreach ($results as $s => $hspInfoArray) {
       $count++;
       $hsp = 0;
       foreach ($hspInfoArray as $hspInfoStr => $e) {
         list($q,$ss,$se,$qs,$qe) = preg_split('/,/',$hspInfoStr);
-        if ($s != NULL and $s != $last_s) {
-          printGFF_parent_children($gff,$IDs);
-         $IDs = array();
+        if ($s != NULL and  $s != $last_s ) {
+          $hsp=0;
         }
         $IDs["$s,$q"]['count']=$count;
         $q_strand = '+';
@@ -789,32 +789,21 @@ function convert_tsv2gff3($blast_tsv,$blast_gff){
         $last_s = $s;
       }
     }
-    printGFF_parent_children($gff,$IDs);
-
-  // Close the files.
-  fclose($tsv);
-  fclose($gff);
-}
-
-/**
- *   printGFF_parent_children
- *   prints the GFF parent feature and all of its children features
- *
- *
- *  @param $blast_feature_array
- *  an array of the all the child features which is used to generate the smallest and largest coordinates for the parent
- *
- *
- */
 
-function printGFF_parent_children ($gff,$blast_feature_array){
-  foreach ($blast_feature_array as $sq => $value ) {
+  // Now can print a parent gff line and all the children.
+  // Note: the evalues seem to be sorted properly without actually sorting them.
+  // @todo: need to make sure this is always true.
+  foreach ($IDs as $sq => $value ) {
     list ($s,$q) = preg_split('/,/' , $sq);
-    $id_count = $blast_feature_array["$s,$q"]['count'];
-    $evalue =  $blast_feature_array["$s,$q"]['E'];
-    $parent =  join ("\t", array($s, "BLASTRESULT" , "match" , $blast_feature_array["$s,$q"]['SS'] , $blast_feature_array["$s,$q"]['SE'] , $blast_feature_array["$s,$q"]['E'] , $blast_feature_array["$s,$q"]['strand'] , '.' , "ID=$s.$id_count;Name=$q($evalue)")) . "\n";
-    $child = join ("\n",$blast_feature_array[$sq]['HSPs']) . "\n";
+    $evalue =  $IDs["$s,$q"]['E'];
+    $count = $IDs["$s,$q"]['count'];
+    $parent =  join ("\t", array($s, "BLASTRESULT" , "match" , $IDs["$s,$q"]['SS'] , $IDs["$s,$q"]['SE'] , $IDs["$s,$q"]['E'] , $IDs["$s,$q"]['strand'] , '.' , "ID=$s.$count;Name=$q($evalue)")) . "\n";
+    $child = join ("\n",$IDs[$sq]['HSPs']) . "\n";
     fwrite($gff,$parent);
     fwrite($gff,$child);
   }
+
+  // Close the files.
+  fclose($tsv);
+  fclose($gff);
 }