Added start of GFF Exporter

tripal_feature/includes/tripal_feature.gff_exporter.inc

@@ -0,0 +1,150 @@
+<?php 
+
+function tripal_feature_gff3_exporter($source, $filters) {
+  
+  $select = "
+    SELECT SF.uniquename as landmark_uname, SF.name as landmark_name,
+      F.feature_id, F.dbxref_id, F.uniquename, F.name, CVT.name as type,
+      FL.fmin, FL.fmax, FL.strand, FL.phase
+  ";
+  $from = "
+    FROM {featureloc} FL
+      INNER JOIN {feature} F on FL.feature_id = F.feature_id
+      INNER JOIN {cvterm} CVT on CVT.cvterm_id = F.type_id
+      INNER JOIN {feature} SF on FL.srcfeature_id = SF.feature_id
+  ";
+  $where = "
+    WHERE 1=1
+  ";
+  $order = "
+    ORDER BY SF.uniquename, FL.fmin
+  ";
+
+  $args = array();
+  if (array_key_exists('genus', $filters) or array_key_exists('species', $filters)) {
+    $from .= "INNER JOIN {organism} O on F.organism_id = O.organism_id ";
+    if (array_key_exists('genus', $filters)) { 
+      $where .= "AND O.genus = :genus ";
+      $args[':genus'] = $filters['genus'];
+    }
+    if (array_key_exists('species', $filters)) {
+      $where .= "AND O.species = :species ";
+      $args[':species'] = $filters['species'];
+    }
+  }
+  
+  if (array_key_exists('types', $filters)) {
+    $where .= "AND CVT.name IN (:types) ";
+    $args[':types'] = $filters['types'];
+  }
+
+  $sql = "$select $from $where $order";
+  
+  // The SQL statement for feature properties.
+  $props_sql = "
+    SELECT CVT.name, FP.value
+    FROM {featureprop} FP
+      INNER JOIN {cvterm} CVT on CVT.cvterm_id = FP.type_id
+    WHERE FP.feature_id = :feature_id
+    ORDER BY CVT.name
+  ";
+  
+  // The SQL statement for Dbxrefs
+  $dbxref_sql = "
+    SELECT DB.name, DBX.accession
+    FROM {dbxref} DBX
+      INNER JOIN {db} DB on DB.db_id = DBX.db_id
+    WHERE DBX.dbxref_id = :dbxref_id
+    UNION
+    SELECT DB.name, DBX.accession
+    FROM {feature_dbxref} FDBX 
+      INNER JOIN {dbxref} DBX on DBX.dbxref_id = FDBX.dbxref_id
+      INNER JOIN {db} DB on DB.db_id = DBX.db_id
+    WHERE FDBX.feature_id = :feature_id
+  ";
+  
+  // The SQL statement for CVTerms
+  $cvterm_sql = "
+    SELECT CV.name as db_name, DBX.accession
+    FROM {feature_cvterm} FCVT
+      INNER JOIN {cvterm} CVT on CVT.cvterm_id = FCVT.cvterm_id
+      INNER JOIN {cv} CV on CV.cv_id = CVT.cv_id
+      INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
+    WHERE FCVT.feature_id = :feature_id
+  ";
+  $results = chado_query($sql, $args);
+  while ($line = $results->fetchObject()) {
+    print $line->landmark_uname . "\t";
+    print $source . "\t";
+    print $line->type . "\t";
+    print $line->fmin . "\t";
+    print $line->fmax . "\t";
+    print "." . "\t";
+    if ($line->strand) {
+      print $line->strand . "\t";
+    } 
+    else {
+      print '.' . "\t";
+    }
+    if ($line->phase) {
+      print $line->phase . "\t";
+    }
+    else {
+      print '.' . "\t";
+    }
+    print "ID=" . $line->uniquename . ";Name=" . $line->name . ";";
+    
+    $props = chado_query($props_sql, array(':feature_id' => $line->feature_id));
+    $prop_name = '';
+    while ($prop = $props->fetchobject()) {
+      // If this is the first time we've encountered this property then
+      // add the name=value key pair.
+      if ($prop_name != $prop->name) {
+        if ($prop_name) {
+          // End the previous property
+          print ";";
+        }
+        // TODO: urlencode the properties
+        print $prop->name . "=" . $prop->value;
+        $prop_name = $prop->name;
+      }
+      // If we've seen this property before then just add the value.
+      else {
+        print "," . $prop->value;
+      }
+    }
+    // End the last property
+    if ($prop_name) {
+      print ";";
+    }
+    
+    // Add in any DBXref records
+    $args = array(
+      ':feature_id' => $line->feature_id,
+      ':dbxref_id' => $line->dbxref_id,
+    );
+    $dbxrefs = chado_query($dbxref_sql, $args);
+    $xrefs = '';
+    while ($dbxref = $dbxrefs->fetchObject()) {
+      $xrefs .= $dbxref->name . ":" . $dbxref->accession . ",";
+    }
+    if ($xrefs) {
+      print "Dbxref=" . substr($xrefs, 0, -1) . ";";
+    }
+    
+    // Add in any CVTerm records
+    $args = array(
+      ':feature_id' => $line->feature_id,
+    );
+    $cvterms = chado_query($cvterm_sql, $args);
+    $xrefs = '';
+    while ($cvterm = $cvterms->fetchObject()) {
+      $xrefs .= $cvterm->db_name . ":" . $cvterm->accession . ",";
+    }
+    if ($xrefs) {
+      print "Ontology_term=" . substr($xrefs, 0, -1) . ";";
+    }
+    
+    print "\n";
+  }
+}