Changed Paths

bin/Modules/Ensembl/ActivityCategorizer.py

@@ -4,21 +4,21 @@
 
 class ActivityCategorizer:
 
-    def __init__(self, release, organism):
+    def __init__(self, release, organism, wd):
 
         # List of all Folders with Activity Tables
 
         self.folderlist = []
 
         # Dictionary from celltypes_organism.json mit key = Kategorie und Value = [Ordner]
 
-        self.c_dict = self.read_config(organism)
+        self.c_dict = self.read_config(organism, wd)
 
         # Activity table from all files as dict
 
         self.activity = {}
 
-        self.get_activity_data(release, organism)
+        self.get_activity_data(release, organism, wd)
 
         # Categorized Activity from Json-config
         print("Categorization: This may take a while")
@@ -29,10 +29,10 @@ def __init__(self, release, organism):
     def get_categorization(self):
         return self.categorization
 
-    def read_config(self, organism):
+    def read_config(self, organism, wd):
 
         c_dict = {}
-        path_to_config = os.path.join("../config/celltypes_"+organism+".json")
+        path_to_config = os.path.join(wd, "../config/celltypes_"+organism+".json")
         with open(path_to_config) as input:
             data = json.loads(input.read())
             for x in data:
@@ -41,11 +41,11 @@ def read_config(self, organism):
 
         return c_dict
 
-    def get_activity_data(self, release, organism):
+    def get_activity_data(self, release, organism, wd):
 
         for folder in self.folderlist:
             # Generate path to binary File
-            file = os.path.join("./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())
 

bin/Modules/Ensembl/ActivityTable.py

@@ -15,8 +15,8 @@ class ActivityTable:
     4, "activity=NA"
     """
 
-    def __init__(self, organism, current_release):
-        self.link = os.path.join("./EnsemblData/", current_release, organism, "activity")
+    def __init__(self, organism, current_release, wd):
+        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",

bin/Modules/Ensembl/Ensembl.py

@@ -1,20 +1,20 @@
-from Modules.Ensembl.ActivityTable import ActivityTable
-from Modules.Ensembl.FTPHandling.VersionChecker import EnsemblRegulationFTPRetriever as FTPRetriever
-from Modules.Ensembl.ActivityCategorizer import ActivityCategorizer
-from Modules.Ensembl.GTFGen import GTFGen
+from bin.Modules.Ensembl.ActivityTable import ActivityTable
+from bin.Modules.Ensembl.FTPHandling.VersionChecker import EnsemblRegulationFTPRetriever as FTPRetriever
+from bin.Modules.Ensembl.ActivityCategorizer import ActivityCategorizer
+from bin.Modules.Ensembl.GTFGen import GTFGen
 
 
 class Ensembl:
 
-    def __init__(self, organism):
+    def __init__(self, organism, wd):
         print("Starting Ensembl")
-        self.updater = FTPRetriever(organism)
+        self.updater = FTPRetriever(organism, wd)
         self.release = self.updater.get_release()
-        self.acttable = ActivityTable(organism, self.release)
+        self.acttable = ActivityTable(organism, self.release, wd)
         self.acttable.check_and_generate_activity_table()
-        self.categorizer = ActivityCategorizer(self.release, organism)
+        self.categorizer = ActivityCategorizer(self.release, organism, wd)
         print("Generating GTF")
-        self.gtf_generator = GTFGen(organism, self.release)
+        self.gtf_generator = GTFGen(organism, self.release, wd)
 
         print("Ensembl Finished !")
 

bin/Modules/Ensembl/FTPHandling/URLRetrieve.py

@@ -1,5 +1,5 @@
 import ftplib
-from Modules.Ensembl.FTPHandling.FTPEntry import FTPEntry
+from bin.Modules.Ensembl.FTPHandling.FTPEntry import FTPEntry
 
 
 class FTPHandler:

bin/Modules/Ensembl/FTPHandling/VersionChecker.py

@@ -1,4 +1,4 @@
-from Modules.Ensembl.FTPHandling.URLRetrieve import FTPHandler
+from bin.Modules.Ensembl.FTPHandling.URLRetrieve import FTPHandler
 import os.path
 
 
@@ -9,12 +9,12 @@ class EnsemblRegulationFTPRetriever:
     And downloading newest version if necessary
     """
 
-    def __init__(self, organism):
+    def __init__(self, organism, wd):
         self.site_ftp = FTPHandler("ftp.ensembl.org", "pub")
         self.remoteversion = self.get_current_ftp_version()
-        self.localversion = self.get_current_local_version()
-        if self.check_version_difference(organism):
-            self.download_currentversion_version(self.remoteversion, organism)
+        self.localversion = self.get_current_local_version(wd)
+        if self.check_version_difference(organism, wd):
+            self.download_currentversion_version(self.remoteversion, organism, wd)
         else:
             print("Newest Version installed, no update needed.")
 
@@ -31,15 +31,15 @@ def get_current_ftp_version(self):
         print("Current release is "+c_release)
         return c_release
 
-    def check_organism(self, organism, release):
-        if organism in next(os.walk("./EnsemblData/"+release+"/"))[1]:
+    def check_organism(self, organism, release, wd):
+        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):
-        directories = next(os.walk("./EnsemblData/"))[1]
+    def get_current_local_version(self, wd):
+        directories = next(os.walk(os.path.join(wd, "/EnsemblData/")))[1]
         for dir in directories:
             if "release" in dir:
                 localversion = sorted(directories, reverse=True)[0]
@@ -51,7 +51,7 @@ def get_current_local_version(self):
         print("No Version installed !")
         return None
 
-    def check_version_difference(self, organism):
+    def check_version_difference(self, organism, wd):
 
         local_version = self.localversion
         remote_version = self.remoteversion
@@ -64,16 +64,16 @@ def check_version_difference(self, organism):
             print("Outdated Version detected ! local: " + local_version + " remote: " + remote_version)
             return True
         else:
-            if self.check_organism(organism, local_version):
+            if self.check_organism(organism, local_version, wd):
                 return True
             else:
                 return False
 
-    def download_currentversion_version(self, version, organism):
+    def download_currentversion_version(self, version, organism, wd):
 
         # Download Base File
 
-        targetfolder = os.path.join("./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)

bin/Modules/Ensembl/GTFGen.py

@@ -5,14 +5,14 @@
 
 class GTFGen:
 
-    def __init__(self, organism, release):
+    def __init__(self, organism, release, wd):
 
-        self.gff_lines = self.get_organism_as_gff(organism, release)
+        self.gff_lines = self.get_organism_as_gff(organism, release, wd)
         self.value_map = {0: "ACTIVE", 1: "POISED", 2: "REPRESSED", 3: "INACTIVE", 4: "NA"}
 
-    def get_organism_as_gff(self, organism, release):
+    def get_organism_as_gff(self, organism, release, wd):
 
-        directory = os.path.join("./EnsemblData/", release, organism)
+        directory = os.path.join(wd, "/EnsemblData/", release, organism)
         inputfile = ""
         for file in os.listdir(directory):
             if file.endswith("gff.gz"):