From abf17d174330d2148106246ac56b08f02bc293d2 Mon Sep 17 00:00:00 2001
From: Nicolas MAILLET <nicolas.maillet@pasteur.fr>
Date: Thu, 26 Apr 2018 18:00:32 +0200
Subject: [PATCH] Changing import

---
 rpg/RapidPeptidesGenerator.py | 14 +++++++-------
 rpg/digest.py                 |  6 +++---
 rpg/enzymes_definition.py     |  4 ++--
 rpg/rule.py                   |  2 +-
 rpg/sequence.py               |  2 +-
 5 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/rpg/RapidPeptidesGenerator.py b/rpg/RapidPeptidesGenerator.py
index 6c90586..e580376 100644
--- a/rpg/RapidPeptidesGenerator.py
+++ b/rpg/RapidPeptidesGenerator.py
@@ -41,10 +41,10 @@ necessary functions
 #Input format : a fasta/fastq file or a sequence
 #Output format : a fasta/csv/tsv file containing the digested sequences
 #@author: Nicolas Maillet
-#@version: 0.0.9α
+#@version: 0.5.1α
 #@note: Pwet
 
-__version_info__ = ('0', '0', '8')
+__version_info__ = ('0', '5', '1')
 __version__ = '.'.join(__version_info__)
 __revision_date__ = "2018-02-28"
 __author__ = "Nicolas Maillet"
@@ -54,10 +54,10 @@ import os
 import sys
 import uuid
 from pathlib import Path
-import core
-import digest
-import enzyme
-from enzymes_definition import AVAILABLE_ENZYMES
+from rpg import core
+from rpg import digest
+from rpg import enzyme
+from rpg.enzymes_definition import AVAILABLE_ENZYMES
 sys.path.insert(0, str(Path.home())) # Home path
 from rpg_user import AVAILABLE_ENZYMES_USER
 
@@ -304,7 +304,7 @@ def main():
 
     # --addenzyme option
     if args.addenzyme:
-        enzyme.user_creation_enzyme()
+        enzyme.user_creation_enzyme(ALL_ENZYMES)
         sys.exit(0)
 
     # --digest option
diff --git a/rpg/digest.py b/rpg/digest.py
index f2bc9ff..383c008 100644
--- a/rpg/digest.py
+++ b/rpg/digest.py
@@ -25,9 +25,9 @@
 """Contains class and function needed to perform a digestion"""
 import os
 import random
-import core
-import rule
-import sequence
+from rpg import core
+from rpg import rule
+from rpg import sequence
 
 class ResultOneDigestion:
     """Result of the digestion of one sequence by one enzyme.
diff --git a/rpg/enzymes_definition.py b/rpg/enzymes_definition.py
index d63bcca..190fcc7 100644
--- a/rpg/enzymes_definition.py
+++ b/rpg/enzymes_definition.py
@@ -23,8 +23,8 @@
 ########################################################################
 
 """Definition of default enzymes in RPG"""
-import enzyme
-import rule
+from rpg import enzyme
+from rpg import rule
 
 AVAILABLE_ENZYMES = []
 
diff --git a/rpg/rule.py b/rpg/rule.py
index b557449..233d008 100644
--- a/rpg/rule.py
+++ b/rpg/rule.py
@@ -27,7 +27,7 @@ cleaving rules
 """
 import re
 from collections import defaultdict
-import core
+from rpg import core
 
 class Rule:
     """Definition of a principal rule defining where a cleavage occurs.
diff --git a/rpg/sequence.py b/rpg/sequence.py
index c94ecf7..dfc389a 100644
--- a/rpg/sequence.py
+++ b/rpg/sequence.py
@@ -23,7 +23,7 @@
 ########################################################################
 
 """Contains classes and function related to sequences"""
-import core
+from rpg import core
 
 class Peptide:
     """Definition of a peptide, containing the header of its original
-- 
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