From e1db4c2a0aeebcc13620e698fbae93ad11c47e78 Mon Sep 17 00:00:00 2001
From: basti <sb@pus.de>
Date: Thu, 3 Jan 2019 16:50:14 +0100
Subject: [PATCH] Added functionality to Fix #19

---
 bin/3.1_create_gtf/Modules/CrossMapper.py |  4 ++--
 bin/3.1_create_gtf/Modules/SaveResults.py | 16 ++++++++--------
 bin/3.1_create_gtf/RegGTFExtractor.py     | 10 +++++++---
 3 files changed, 17 insertions(+), 13 deletions(-)

diff --git a/bin/3.1_create_gtf/Modules/CrossMapper.py b/bin/3.1_create_gtf/Modules/CrossMapper.py
index 7e8c259..293783a 100644
--- a/bin/3.1_create_gtf/Modules/CrossMapper.py
+++ b/bin/3.1_create_gtf/Modules/CrossMapper.py
@@ -15,10 +15,10 @@ class CrossMapper:
     def __init__(self, org, wd, out, is_dir):
         self.org = org
         if is_dir:
-            self.infile = os.path.join( wd + "/temp/" + org + ".gtf")
+            self.infile = os.path.join(wd + "/temp/" + org + ".gtf")
         else:
             self.infile = os.path.join(wd+"/data/temp/"+org+".gtf")
-        self.outfile = os.path.join(out+"/" + org + "_mapped.gtf")
+        self.outfile = os.path.join(out)
         self.chainfile = self.get_chain_file(org, wd, is_dir)
 
         # Execute Crossmapper for gff/gtf files
diff --git a/bin/3.1_create_gtf/Modules/SaveResults.py b/bin/3.1_create_gtf/Modules/SaveResults.py
index ec5ed61..8c7b645 100644
--- a/bin/3.1_create_gtf/Modules/SaveResults.py
+++ b/bin/3.1_create_gtf/Modules/SaveResults.py
@@ -14,7 +14,7 @@ class ResultSaver:
 
     """
 
-    def __init__(self, results, organism, wd,  mapped, is_data_dir, tissue, out):
+    def __init__(self, results, organism, wd,  mapped, is_data_dir, out):
 
         # Constructor and main method for result-saving
         # input_parameter: results     = finished list of gtf-entries
@@ -24,20 +24,20 @@ def __init__(self, results, organism, wd,  mapped, is_data_dir, tissue, out):
         #                  is_data_dir = boolean if wd is a data_dir (true) or not (false)
         #                  is_data_dir = boolean if wd is a data_dir (true) or not (false)
 
-
-        # TODO: DATADIR !!
-
         print("Save results to File !")
         self.path = ""
+
+        # If results has to be crossmapped -> Path is tempdirectory.
+
         if mapped:
             if is_data_dir:
                 self.path = os.path.join(wd + "/temp/" + organism + ".gtf")
             else:
-                self.path = os.path.join(wd + "/data/temp/" + organism + ".gtf" )
-        elif tissue:
-            self.path = os.path.join(out+"/"+organism+"_filtered.gtf")
+                self.path = os.path.join(wd + "/data/temp/" + organism + ".gtf")
+
+        # if no crossmapping is needed:
         else:
-            self.path = os.path.join(out+"/"+organism+".gtf")
+            self.path = os.path.join(out)
 
         with open(self.path, "w") as output_file:
             for line in results:
diff --git a/bin/3.1_create_gtf/RegGTFExtractor.py b/bin/3.1_create_gtf/RegGTFExtractor.py
index 1c6a05f..9286151 100644
--- a/bin/3.1_create_gtf/RegGTFExtractor.py
+++ b/bin/3.1_create_gtf/RegGTFExtractor.py
@@ -103,6 +103,10 @@ def main_script(organism, wd, data_dir, out, tissuetype=None):
     # main function
     # input_parameter: all parameters from argparse
 
+    # if no output parameter is given output file is "./organism.gtf"
+    if out == ".":
+        out = "./"+organism+".gtf"
+
     (org,  x_mappable) = check_organism(organism)
     if not data_dir:
         check_for_local_folder(wd)
@@ -122,11 +126,11 @@ def main_script(organism, wd, data_dir, out, tissuetype=None):
     print("Getting Unique Results")
     unique_filter = UniqueFilter(ense.get_gtf(), ucsc.get_gtf(), tissues)
     if data_dir:
-        ResultSaver(unique_filter.get_results(), organism, data_dir, x_mappable, True, tissues, out)
+        ResultSaver(unique_filter.get_results(), organism, data_dir, x_mappable, True, out)
         if x_mappable:
             CrossMapper(organism, data_dir, out, True)
     else:
-        ResultSaver(unique_filter.get_results(), organism, wd, x_mappable, False, tissues, out)
+        ResultSaver(unique_filter.get_results(), organism, wd, x_mappable, False, out)
         if x_mappable:
             CrossMapper(organism, wd, out, False)
 
@@ -140,7 +144,7 @@ def main_script(organism, wd, data_dir, out, tissuetype=None):
     parser.add_argument('--tissue', help='Tissue- or Celltype(s)', action='store', nargs='*', type=str)
     parser.add_argument('--wd', help='Working directory. default: "."', action='store', default=os.getcwd(), type=str)
     parser.add_argument('--dir', help='Data directory. default: "working_directory"', action='store', default="", type=str)
-    parser.add_argument('--out', help='Output directory: default: "."', action='store', default=".", type=str)
+    parser.add_argument('--out', help='Path to output file: default: "./organism.gtf"', action='store', default=".", type=str)
     args = vars(parser.parse_args())
 
     # Check if organism exists