0008-Add-simple-sequence-controller-and-view.patch

From 3d99d6c919208add440b0d38a43c5019661ae711 Mon Sep 17 00:00:00 2001
From: Martin Ernstsen <martin.ernstsen@gmail.com>
Date: Thu, 28 Feb 2013 17:59:55 +0100
Subject: [PATCH 08/12] Add simple sequence controller and view

The sequence controller can extract a sequence from a Blastdb sequence
store at a specified location. The view will give a bare-bones view
of the sequence in fasta format.
---
 app/controllers/sequences_controller.php |   64 ++++++++++++++++++++++++++++++
 app/views/sequences/view.ctp             |   25 ++++++++++++
 2 files changed, 89 insertions(+), 0 deletions(-)
 create mode 100644 app/controllers/sequences_controller.php
 create mode 100644 app/views/sequences/view.ctp

diff --git a/app/controllers/sequences_controller.php b/app/controllers/sequences_controller.php
new file mode 100644
index 0000000..18b4923
--- /dev/null
+++ b/app/controllers/sequences_controller.php
@@ -0,0 +1,64 @@
+<?php
+/*
+ * Controller that can extract a sequence from a Blastdb sequence store. The
+ * sequence store must have the following path:
+ *     SEQUENCE_STORE_PATH/$projectId/$dataset/$dataset
+ * For example, if $projectId is 2, and the dataset is named VSTall, the
+ * path becomes:
+ *     SEQUENCE_STORE_PATH/2/VSTall/VSTall
+ *
+ * The peptide_id must follow Norstruct naming convention, which is of the form:
+ *     contig1234_orf6789
+ **/
+
+class SequencesController extends AppController {
+    var $name = 'Sequences';
+    var $uses = array();
+    var $components = array('Solr');
+
+    function view() {
+        $this->layout = 'empty';
+        $this->pageTitle = 'tullball';
+
+        // Get dataset and peptide id from named url parameters
+        $named_params = $this->params['named'];
+        $dataset = $named_params['dataset'];
+        $peptideId = $named_params['peptide_id'];
+
+        // Get project id needed for path to sequence store
+		$this->loadModel('Project');
+        $projectId = $this->Project->getProjectId($dataset);
+        $this->log("project id: "."$projectId");
+
+        // For the MetaPipe pipeline, peptide_id is on the form: contig01116_orf00003.
+        // To search the sequence store, the contig part must be retrieved
+        $tmp = explode('_', $peptideId);
+        $contig = $tmp[0];
+        
+        // Get the whole contig sequence
+        $commandContig = FASTACMD_PATH." -d ".SEQUENCE_STORE_PATH."/$projectId/$dataset/$dataset -s $contig";
+		exec($commandContig, $outputContig);
+        $outputContig[0] = str_replace(">lcl|", ">", $outputContig[0]);
+        $this->set('full_sequence', $outputContig);
+
+        // If the peptide has start and end information, retrieve ORF from full contig
+        if (isset($named_params['orf_start']) && isset($named_params['orf_end'])) {
+            $orf_start = $named_params['orf_start'];
+            $orf_end = $named_params['orf_end'];
+
+            // If orf_start and orf_end are specified, make sure orf_start is lowest
+            if ($orf_end < $orf_start) {
+                $tmp = $orf_start;
+                $orf_start = $orf_end;
+                $orf_end = $tmp;
+            }
+            // Get the ORF sequence
+            $commandOrf = FASTACMD_PATH." -d ".SEQUENCE_STORE_PATH."/$projectId/$dataset/$dataset -s $contig -L $orf_start,$orf_end";
+            exec($commandOrf, $outputOrf);
+            $outputOrf[0] = str_replace(">lcl|", ">", $outputOrf[0]);
+            $this->set('orf_sequence', $outputOrf);
+        }
+        $this->set('peptide_id', $peptideId);
+    }
+}
+?>
diff --git a/app/views/sequences/view.ctp b/app/views/sequences/view.ctp
new file mode 100644
index 0000000..768e50b
--- /dev/null
+++ b/app/views/sequences/view.ctp
@@ -0,0 +1,25 @@
+<title><?php echo($peptide_id);?></title>
+<h1><?php echo($peptide_id);?></h1>
+
+<h2>ORF</h2>
+<pre>
+<?php
+if (isset($orf_sequence)) {
+    foreach ($orf_sequence as $line) {
+        echo($line."\n");
+    }
+}
+else {
+    echo("Start and end postition not available");
+}
+?>
+</pre>
+
+<h2>Full Contig</h2>
+<pre>
+<?php
+foreach ($full_sequence as $line) {
+    echo($line."\n");
+}
+?>
+</pre>
-- 
1.7.4.1