From b3223d11b1f2f46c460ab464866ecdfb5732dd28 Mon Sep 17 00:00:00 2001
From: basti <sb@pus.de>
Date: Sun, 6 Jan 2019 15:31:40 +0100
Subject: [PATCH] Added Validator -> Fix #32

---
 bin/3.1_create_gtf/Modules/Validator.py | 35 +++++++++++++++++++++++++
 bin/3.1_create_gtf/RegGTFExtractor.py   |  5 ++++
 2 files changed, 40 insertions(+)
 create mode 100644 bin/3.1_create_gtf/Modules/Validator.py

diff --git a/bin/3.1_create_gtf/Modules/Validator.py b/bin/3.1_create_gtf/Modules/Validator.py
new file mode 100644
index 0000000..55c03e0
--- /dev/null
+++ b/bin/3.1_create_gtf/Modules/Validator.py
@@ -0,0 +1,35 @@
+class Validator:
+
+    """
+        Class to validate the gtf-output-file.
+        @author: Sebastian Beyvers
+        @contact: sebastian.beyvers@med.uni-giessen.de
+
+    """
+
+    def __init__(self, out_file):
+
+        # Constructor
+        # input_parameter: out_file = Path to Outputfile
+
+        self.out_file = out_file
+        self.test_read_file()
+
+    def test_read_file(self):
+
+        # Method to testread the file
+
+        with open(self.out_file) as outfile:
+            line = outfile.readline()
+
+            if line:
+                if len(line.split("\t")) == 9:
+                    print("Check successfull !")
+                else:
+                    print("Incorrect output Format: Try again after deleting data folder.")
+            else:
+                print("Outputfile not in correct Format: Try again after deleting data Folder.")
+                exit(1)
+
+# Debug
+# v = Validator("/home/basti/Schreibtisch/test_hg38.gtf")
\ No newline at end of file
diff --git a/bin/3.1_create_gtf/RegGTFExtractor.py b/bin/3.1_create_gtf/RegGTFExtractor.py
index 9286151..9000341 100644
--- a/bin/3.1_create_gtf/RegGTFExtractor.py
+++ b/bin/3.1_create_gtf/RegGTFExtractor.py
@@ -14,6 +14,7 @@
 from Modules.Uniquifier import UniqueFilter
 from Modules.SaveResults import ResultSaver
 from Modules.CrossMapper import CrossMapper
+from Modules.Validator import Validator
 import os
 import json
 
@@ -134,6 +135,10 @@ def main_script(organism, wd, data_dir, out, tissuetype=None):
         if x_mappable:
             CrossMapper(organism, wd, out, False)
 
+    # Validate outputfile
+
+    Validator(out)
+
 
 if __name__ == '__main__':