diff --git a/rpg/RapidPeptidesGenerator.py b/rpg/RapidPeptidesGenerator.py index 6c905869639133aa832006f046bdb210b11f8db1..e580376c65c0397bfe46489dccf2920e28681492 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 f2bc9ff76ac7a06af500971cdb784de56d0bc1d8..383c008e0172296fb283375a577f084a230efb8c 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 d63bcca94bd40974f541ea0eb90b74b7e971dbe6..190fcc7158e7091a7faed3df53fa0aacc543c370 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 b557449c2a51772f2dafa3e808e545b3071964f7..233d008d7cf01cbd367d5ffcc376e9f0bcfe429c 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 c94ecf751509fd196dd29b6bad323f007282e718..dfc389a5c6315acf8b0aa8e6f0752792d58f31db 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