Remove unused imports. Update Readme. Factorize goto_species_dir()

README.md

@@ -149,8 +149,9 @@ Directory tree structure:
 
 [BSD 3-Clause](./LICENSE)
 
-## Acknowledgments
+## Contributors
 
-[Anthony Bretaudeau](https://github.com/abretaud)
-
-[Matéo Boudet](https://github.com/mboudet)
\ No newline at end of file
+- [Matéo Boudet](https://github.com/mboudet)
+- [Anthony Bretaudeau](https://github.com/abretaud)
+- [Loraine Brillet-Guéguen](https://github.com/loraine-gueguen)
+- [Arthur Le Bars](https://gitlab.com/Troubardours)
\ No newline at end of file

gga_get_data.py

 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
-import bioblend
 import argparse
 import os
-import subprocess
 import logging
 import sys
-import fnmatch
 import time
-import json
-import re
-import stat
 import shutil
 
-from bioblend.galaxy.objects import GalaxyInstance
-from bioblend import galaxy
-
 import utilities
 import speciesData
 
@@ -36,24 +27,6 @@ class GetData(speciesData.SpeciesData):
 
     """
 
-    def goto_species_dir(self):
-        """
-        Go to the species directory (starting from the main dir)
-
-        :return:
-        """
-
-        os.chdir(self.main_dir)
-        species_dir = os.path.join(self.main_dir, self.genus_species) + "/"
-        try:
-            os.chdir(species_dir)
-        except OSError:
-            logging.critical("Cannot access %s" % species_dir)
-            sys.exit(0)
-        return 1
-
-
-
     def make_directory_tree(self):
         """
         Generate the directory tree for an organism

gga_init.py

@@ -11,7 +11,7 @@ import yaml
 import shutil
 
 from pathlib import Path
-from jinja2 import Template, Environment, FileSystemLoader
+from jinja2 import Environment, FileSystemLoader
 
 import utilities
 import speciesData

speciesData.py

@@ -4,6 +4,7 @@
 import os
 import sys
 import utilities
+import logging
 
 from _datetime import datetime
 
@@ -15,6 +16,22 @@ class SpeciesData:
 
     """
 
+    def goto_species_dir(self):
+        """
+        Go to the species directory (starting from the main dir)
+
+        :return:
+        """
+
+        os.chdir(self.main_dir)
+        species_dir = os.path.join(self.main_dir, self.genus_species) + "/"
+        try:
+            os.chdir(species_dir)
+        except OSError:
+            logging.critical("Cannot access %s" % species_dir)
+            sys.exit(0)
+        return 1
+
     def clean_string(self, string):
         if not string is None and string != "":
             clean_string = string.replace(" ", "_").replace("-", "_").replace("(", "").replace(")", "").replace("'", "").strip()