Fixed: "Paths" V2

loosolab · Dec 4, 2018 · d22a0e1 · d22a0e1
1 parent 8c843fb
commit d22a0e1
Show file tree

Hide file tree

Showing 7 changed files with 17 additions and 17 deletions.
diff --git a/bin/Modules/Ensembl/ActivityCategorizer.py b/bin/Modules/Ensembl/ActivityCategorizer.py
@@ -32,7 +32,7 @@ def get_categorization(self):
     def read_config(self, organism, wd):
 
         c_dict = {}
-        path_to_config = os.path.join(wd, "/config/celltypes_"+organism+".json")
+        path_to_config = os.path.join(wd +"/config/celltypes_"+organism+".json")
         with open(path_to_config) as input_file:
             data = json.loads(input_file.read())
             for x in data:
@@ -45,7 +45,7 @@ def get_activity_data(self, release, organism, wd):
 
         for folder in self.folderlist:
             # Generate path to binary File
-            file = os.path.join(wd, "/EnsemblData", release, organism, "activity", folder, "table.bin")
+            file = os.path.join(wd + "/EnsemblData", release, organism, "activity", folder, "table.bin")
             with open(file, "rb") as tables:
                 self.activity[folder] = bytearray(tables.read())
 

diff --git a/bin/Modules/Ensembl/ActivityTable.py b/bin/Modules/Ensembl/ActivityTable.py
@@ -16,7 +16,7 @@ class ActivityTable:
     """
 
     def __init__(self, organism, current_release, wd):
-        self.link = os.path.join(wd, "/EnsemblData/", current_release, organism, "activity")
+        self.link = os.path.join(wd + "/EnsemblData/", current_release, organism, "activity")
         self.folders = next(os.walk(self.link))[1]
         self.generator = ATGenerator(["activity=ACTIVE",
                                "activity=POISED",

diff --git a/bin/Modules/Ensembl/FTPHandling/VersionChecker.py b/bin/Modules/Ensembl/FTPHandling/VersionChecker.py
@@ -32,14 +32,14 @@ def get_current_ftp_version(self):
         return c_release
 
     def check_organism(self, organism, release, wd):
-        if organism in next(os.walk(os.path.join(wd, "/EnsemblData/"+release+"/")))[1]:
+        if organism in next(os.walk(os.path.join(wd+"/EnsemblData/"+release+"/")))[1]:
             return False
         else:
             print("No Local Version for "+organism+" installed. Installing...")
             return True
 
     def get_current_local_version(self, wd):
-        directories = next(os.walk(os.path.join(wd, "/EnsemblData/")))[1]
+        directories = next(os.walk(os.path.join(wd+"/EnsemblData/")))[1]
         for dir in directories:
             if "release" in dir:
                 localversion = sorted(directories, reverse=True)[0]
@@ -73,7 +73,7 @@ def download_currentversion_version(self, version, organism, wd):
 
         # Download Base File
 
-        targetfolder = os.path.join(wd, "/EnsemblData/", version, organism)
+        targetfolder = os.path.join(wd+"/EnsemblData/", version, organism)
         os.makedirs(targetfolder)
         folder_url = "/pub/"+version+"/regulation/"+organism+"/"
         self.site_ftp.change_dir(folder_url)

diff --git a/bin/Modules/Ensembl/GTFGen.py b/bin/Modules/Ensembl/GTFGen.py
@@ -12,7 +12,7 @@ def __init__(self, organism, release, wd):
 
     def get_organism_as_gff(self, organism, release, wd):
 
-        directory = os.path.join(wd, "/EnsemblData/", release, organism)
+        directory = os.path.join(wd + "/EnsemblData/", release, organism)
         inputfile = ""
         for file in os.listdir(directory):
             if file.endswith("gff.gz"):

diff --git a/bin/Modules/SaveResults.py b/bin/Modules/SaveResults.py
@@ -9,9 +9,9 @@ def __init__(self, results, organism, tissue, wd):
         print("Save results to File !")
         self.path = ""
         if tissue:
-            self.path = os.path.join(wd, "/"+organism+"_filtered.gtf")
+            self.path = os.path.join(wd+"/"+organism+"_filtered.gtf")
         else:
-            self.path = os.path.join(wd, "./"+organism+".gtf")
+            self.path = os.path.join(wd+"/"+organism+".gtf")
 
         with open(self.path, "w") as file:
             write_it = csv.writer(file, delimiter='\t')

diff --git a/bin/Modules/ucsc/ucsc.py b/bin/Modules/ucsc/ucsc.py
@@ -10,8 +10,8 @@ class UcscGtf:
     def __init__(self, org, wd):
         self.organism_id = self.get_organism_id(org)
         self.link = "http://hgdownload.soe.ucsc.edu/gbdb/"+self.organism_id+"/ncbiRefSeq/refSeqFuncElems.bb"
-        self.output = os.path.join(wd, "/UCSCData/"+self.organism_id+".bed")
-        self.path_to_bin = os.path.join(wd, "/Modules/ucsc/bigBedToBed")
+        self.output = os.path.join(wd + "/UCSCData/"+self.organism_id+".bed")
+        self.path_to_bin = os.path.join(wd + "/Modules/ucsc/bigBedToBed")
         print("Getting UCSC Data")
         print("Path to Bin: " + self.path_to_bin)
         self.generate_gff_file()
@@ -68,7 +68,7 @@ def get_organism_id(org):
 
     @staticmethod
     def get_activity_categories(organism, wd):
-        path_to_config = os.path.join(wd, "/config/celltypes_" + organism + ".json")
+        path_to_config = os.path.join(wd+"/config/celltypes_" + organism + ".json")
         categories = {}
         with open(path_to_config) as input_file:
             data = json.loads(input_file.read())
@@ -78,4 +78,4 @@ def get_activity_categories(organism, wd):
         return categories
 
     def get_gtf(self):
-        return self.gtf_lines
+        return self.gtf_lines
diff --git a/bin/RegGTFExtractor.py b/bin/RegGTFExtractor.py
@@ -10,12 +10,12 @@
 
 def check_for_local_folder(wd):
 
-    if not os.path.isdir(os.path.join(wd, "/EnsemblData")):
+    if not os.path.isdir(os.path.join(wd+"/EnsemblData")):
 
-        os.mkdir(os.path.join(wd, "/EnsemblData"))
+        os.mkdir(os.path.join(wd+"/EnsemblData"))
 
-    if not os.path.isdir(os.path.join(wd, "/UCSCData" )):
-        os.mkdir(os.path.join(wd, "/UCSCData" ))
+    if not os.path.isdir(os.path.join(wd+"/UCSCData" )):
+        os.mkdir(os.path.join(wd+"/UCSCData" ))
 
 
 def main_script(org, wd, tissuetype=None):