From f78f16f21eaf3d53dd5c86aad6bebfc72569ca1f Mon Sep 17 00:00:00 2001
From: Yoann Dufresne <yoann.dufresne0@gmail.com>
Date: Mon, 13 Jan 2020 13:23:08 +0100
Subject: [PATCH] refactoring of the code to match package tree
---
README.md | 10 +
deconvolution/d2graph/__init__.py | 0
deconvolution/d2graph/d2_algorithms.py | 2 +-
deconvolution/d2graph/d2_graph.py | 4 +-
deconvolution/d2graph/d2_reduction.py | 3 +-
deconvolution/d2graph/path_algorithms.py | 2 +-
deconvolution/d2graph/path_optimization.py | 3 +-
deconvolution/dgraph/FixedDGIndex.py | 3 +-
deconvolution/dgraph/VariableDGIndex.py | 3 +-
deconvolution/dgraph/d_graph.py | 182 +++++++++---------
deconvolution/main/__init__.py | 0
deconvolution/main/d2_to_path.py | 2 +-
.../main/generate_fake_barcode_graph.py | 4 +-
.../main/generate_fake_molecule_graph.py | 2 +-
deconvolution/main/to_d2_graph.py | 2 +-
setup.py | 10 +
tests/Index_test.py | 10 +-
tests/d2_graph_test.py | 6 +-
tests/d_graph_test.py | 4 +-
tests/graph_manipulation_test.py | 2 +-
20 files changed, 138 insertions(+), 116 deletions(-)
create mode 100644 deconvolution/d2graph/__init__.py
create mode 100644 deconvolution/main/__init__.py
diff --git a/README.md b/README.md
index c2d2075..b9f7294 100644
--- a/README.md
+++ b/README.md
@@ -2,6 +2,16 @@
Trying to deconvolve single tag assignment for multiple molecules
+## Installation
+
+Install the package from the root directory.
+```bash
+ # For users
+ pip install . --user
+ # For developers
+ pip install -e . --user
+```
+
## Scripts
For the majority of the scripts, argparse is used.
diff --git a/deconvolution/d2graph/__init__.py b/deconvolution/d2graph/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/deconvolution/d2graph/d2_algorithms.py b/deconvolution/d2graph/d2_algorithms.py
index 1391181..f54df13 100644
--- a/deconvolution/d2graph/d2_algorithms.py
+++ b/deconvolution/d2graph/d2_algorithms.py
@@ -1,6 +1,6 @@
import networkx as nx
-from d2graph.d2_path import Unitig
+from deconvolution.d2graph.d2_path import Unitig
""" Remove unnecessary transitions
diff --git a/deconvolution/d2graph/d2_graph.py b/deconvolution/d2graph/d2_graph.py
index fc2c27f..f7d6a77 100644
--- a/deconvolution/d2graph/d2_graph.py
+++ b/deconvolution/d2graph/d2_graph.py
@@ -3,8 +3,8 @@ import itertools
from bidict import bidict
import sys
-from dgraph.FixedDGIndex import FixedDGIndex
-from dgraph.d_graph import Dgraph, compute_all_max_d_graphs, list_domination_filter
+from deconvolution.dgraph.FixedDGIndex import FixedDGIndex
+from deconvolution.dgraph.d_graph import Dgraph, compute_all_max_d_graphs
class D2Graph(nx.Graph):
diff --git a/deconvolution/d2graph/d2_reduction.py b/deconvolution/d2graph/d2_reduction.py
index dd534ac..3e02506 100755
--- a/deconvolution/d2graph/d2_reduction.py
+++ b/deconvolution/d2graph/d2_reduction.py
@@ -4,7 +4,8 @@ import networkx as nx
import argparse
import sys
-from d2graph import d2_algorithms as d2a, d2_graph as d2
+from deconvolution.d2graph import d2_graph as d2
+from deconvolution.d2graph import d2_algorithms as d2a
def parse_arguments():
diff --git a/deconvolution/d2graph/path_algorithms.py b/deconvolution/d2graph/path_algorithms.py
index e22c93c..d10a49c 100644
--- a/deconvolution/d2graph/path_algorithms.py
+++ b/deconvolution/d2graph/path_algorithms.py
@@ -1,4 +1,4 @@
-from d2graph.d2_path import Path
+from deconvolution.d2graph.d2_path import Path
""" Greedy algorithm. Start with th most probable unitig (ie lowest normalized penalty first and largest unitig for
equalities). Then extends on both side to the nearest interesting unitig.
diff --git a/deconvolution/d2graph/path_optimization.py b/deconvolution/d2graph/path_optimization.py
index 180f07b..3dbde86 100644
--- a/deconvolution/d2graph/path_optimization.py
+++ b/deconvolution/d2graph/path_optimization.py
@@ -1,7 +1,8 @@
import random
-from d2graph.d2_path import Path
import networkx as nx
+from deconvolution.d2graph.d2_path import Path
+
class Optimizer:
diff --git a/deconvolution/dgraph/FixedDGIndex.py b/deconvolution/dgraph/FixedDGIndex.py
index a9860cc..8edca62 100644
--- a/deconvolution/dgraph/FixedDGIndex.py
+++ b/deconvolution/dgraph/FixedDGIndex.py
@@ -1,6 +1,7 @@
-from dgraph.AbstractDGIndex import AbstractDGIndex
from itertools import combinations
+from deconvolution.dgraph.AbstractDGIndex import AbstractDGIndex
+
class FixedDGIndex(AbstractDGIndex):
diff --git a/deconvolution/dgraph/VariableDGIndex.py b/deconvolution/dgraph/VariableDGIndex.py
index 7809bb0..013bb99 100644
--- a/deconvolution/dgraph/VariableDGIndex.py
+++ b/deconvolution/dgraph/VariableDGIndex.py
@@ -1,6 +1,7 @@
-from dgraph.AbstractDGIndex import AbstractDGIndex
from itertools import combinations
+from deconvolution.dgraph.AbstractDGIndex import AbstractDGIndex
+
class VariableDGIndex(AbstractDGIndex):
diff --git a/deconvolution/dgraph/d_graph.py b/deconvolution/dgraph/d_graph.py
index 5d10b0c..e07ded4 100644
--- a/deconvolution/dgraph/d_graph.py
+++ b/deconvolution/dgraph/d_graph.py
@@ -1,8 +1,8 @@
import networkx as nx
from functools import total_ordering
-import community # pip install python-louvain
+import community # pip install python-louvain TODO: Ajouter dans les requirements !!!
-from dgraph.FixedDGIndex import FixedDGIndex
+from deconvolution.dgraph.FixedDGIndex import FixedDGIndex
@total_ordering
@@ -312,92 +312,92 @@ def compute_all_max_d_graphs(graph, debug=False, clique_mode=None):
return d_graphs
-""" Add the new dg in the dgs list. If dg is dominated by another dg in the list, then it's
- dropped. If any dg in the list is dominated by the dg to add, then, the new dg is added and
- all the dominated dg are removed from the list.
- @param dg A new dg to add/filter.
- @param undominated_dgs_list A list of dg where any of them is dominated by another one.
- @return The updated undominated list.
-"""
-def add_new_dg_regarding_domination(dg, undominated_dgs_list):
- to_remove = []
- dominated = False
-
- # Search for domination relations
- for u_dg in undominated_dgs_list:
- if not dominated and dg.is_dominated(u_dg):
- dominated = True
- if u_dg.is_dominated(dg):
- to_remove.append(u_dg)
-
- # Remove dominated values
- size = len(undominated_dgs_list)
- for dg2 in to_remove:
- undominated_dgs_list.remove(dg2)
-
- # Add the new dg
- if not dominated:
- undominated_dgs_list.append(dg)
-
- return undominated_dgs_list
-
-
-
-def filter_dominated(d_graphs, overall=False, in_place=True):
- if not overall:
- return local_domination_filter(d_graphs, in_place)
-
- all_d_graphs = []
- for dgs in d_graphs.values():
- all_d_graphs.extend(dgs)
-
- all_d_graphs = list_domination_filter(all_d_graphs)
-
- return d_graphs
-
-
-""" Filter the d-graphs by node. In a list of d-graph centered on a node n, if a d-graph is
- completely included in another and have a highest distance score to the optimal, then it is
- filtered out.
- @param d_graphs All the d-graphs to filter, sorted by central node.
- @param in_place If true, modify the content of d_graph with the filtered version. If False,
- copy all the content in a new dictionary.
- @return The filtered dictionary of d-graph per node.
-"""
-def local_domination_filter(d_graphs, in_place=True):
- filtered = d_graphs if in_place else {}
-
- # Filter node by node
- for node, d_graph_list in d_graphs.items():
- lst = str(sorted([str(x) for x in d_graph_list]))
- filtered[node] = brutal_list_domination_filter(d_graph_list, node_name=str(node))
-
- return filtered
-
-
-""" Filter the input d-graphs list. In the list of d-graph centered on a node n, if a d-graph is
- completely included in another and have a highest distance score to the optimal, then it is
- filtered out.
- @param d_graphs All the d-graphs to filter.
- @return The filtered dictionary of d-graph per node.
-"""
-def list_domination_filter(d_graphs):
- filtered = []
-
- # Filter d-graph by d-graph
- for dg in d_graphs:
- add_new_dg_regarding_domination(dg, filtered)
-
- return set(filtered)
-
-def brutal_list_domination_filter(d_graphs, node_name=""):
- undominated = set(d_graphs)
- to_remove = set()
-
- for dg1 in d_graphs:
- for dg2 in d_graphs:
- if dg1.is_dominated(dg2):
- to_remove.add(dg1)
- break
-
- return undominated - to_remove
+# """ Add the new dg in the dgs list. If dg is dominated by another dg in the list, then it's
+# dropped. If any dg in the list is dominated by the dg to add, then, the new dg is added and
+# all the dominated dg are removed from the list.
+# @param dg A new dg to add/filter.
+# @param undominated_dgs_list A list of dg where any of them is dominated by another one.
+# @return The updated undominated list.
+# """
+# def add_new_dg_regarding_domination(dg, undominated_dgs_list):
+# to_remove = []
+# dominated = False
+#
+# # Search for domination relations
+# for u_dg in undominated_dgs_list:
+# if not dominated and dg.is_dominated(u_dg):
+# dominated = True
+# if u_dg.is_dominated(dg):
+# to_remove.append(u_dg)
+#
+# # Remove dominated values
+# size = len(undominated_dgs_list)
+# for dg2 in to_remove:
+# undominated_dgs_list.remove(dg2)
+#
+# # Add the new dg
+# if not dominated:
+# undominated_dgs_list.append(dg)
+#
+# return undominated_dgs_list
+#
+#
+#
+# def filter_dominated(d_graphs, overall=False, in_place=True):
+# if not overall:
+# return local_domination_filter(d_graphs, in_place)
+#
+# all_d_graphs = []
+# for dgs in d_graphs.values():
+# all_d_graphs.extend(dgs)
+#
+# all_d_graphs = list_domination_filter(all_d_graphs)
+#
+# return d_graphs
+#
+#
+# """ Filter the d-graphs by node. In a list of d-graph centered on a node n, if a d-graph is
+# completely included in another and have a highest distance score to the optimal, then it is
+# filtered out.
+# @param d_graphs All the d-graphs to filter, sorted by central node.
+# @param in_place If true, modify the content of d_graph with the filtered version. If False,
+# copy all the content in a new dictionary.
+# @return The filtered dictionary of d-graph per node.
+# """
+# def local_domination_filter(d_graphs, in_place=True):
+# filtered = d_graphs if in_place else {}
+#
+# # Filter node by node
+# for node, d_graph_list in d_graphs.items():
+# lst = str(sorted([str(x) for x in d_graph_list]))
+# filtered[node] = brutal_list_domination_filter(d_graph_list, node_name=str(node))
+#
+# return filtered
+#
+#
+# """ Filter the input d-graphs list. In the list of d-graph centered on a node n, if a d-graph is
+# completely included in another and have a highest distance score to the optimal, then it is
+# filtered out.
+# @param d_graphs All the d-graphs to filter.
+# @return The filtered dictionary of d-graph per node.
+# """
+# def list_domination_filter(d_graphs):
+# filtered = []
+#
+# # Filter d-graph by d-graph
+# for dg in d_graphs:
+# add_new_dg_regarding_domination(dg, filtered)
+#
+# return set(filtered)
+#
+# def brutal_list_domination_filter(d_graphs, node_name=""):
+# undominated = set(d_graphs)
+# to_remove = set()
+#
+# for dg1 in d_graphs:
+# for dg2 in d_graphs:
+# if dg1.is_dominated(dg2):
+# to_remove.add(dg1)
+# break
+#
+# return undominated - to_remove
diff --git a/deconvolution/main/__init__.py b/deconvolution/main/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/deconvolution/main/d2_to_path.py b/deconvolution/main/d2_to_path.py
index 444a14f..667f0c1 100755
--- a/deconvolution/main/d2_to_path.py
+++ b/deconvolution/main/d2_to_path.py
@@ -4,7 +4,7 @@ import networkx as nx
import argparse
import sys
-from d2graph import d2_graph as d2, path_optimization as po
+from deconvolution.d2graph import d2_graph as d2, path_optimization as po
def parse_arguments():
diff --git a/deconvolution/main/generate_fake_barcode_graph.py b/deconvolution/main/generate_fake_barcode_graph.py
index f61631d..9d218af 100755
--- a/deconvolution/main/generate_fake_barcode_graph.py
+++ b/deconvolution/main/generate_fake_barcode_graph.py
@@ -1,10 +1,10 @@
#!/usr/bin/env python3
-import networkx as nx
+import networkx as nx
import random
import argparse
-from dgraph import graph_manipulator as gm
+import deconvolution.dgraph.graph_manipulator as gm
def parse_arguments():
diff --git a/deconvolution/main/generate_fake_molecule_graph.py b/deconvolution/main/generate_fake_molecule_graph.py
index a859ff5..be09663 100755
--- a/deconvolution/main/generate_fake_molecule_graph.py
+++ b/deconvolution/main/generate_fake_molecule_graph.py
@@ -2,7 +2,7 @@
import argparse
-from dgraph import graph_manipulator as gm
+from deconvolution.dgraph import graph_manipulator as gm
def parse_arguments():
diff --git a/deconvolution/main/to_d2_graph.py b/deconvolution/main/to_d2_graph.py
index 4a2d1be..dc409ac 100755
--- a/deconvolution/main/to_d2_graph.py
+++ b/deconvolution/main/to_d2_graph.py
@@ -4,7 +4,7 @@ import networkx as nx
import argparse
import sys
-from d2graph import d2_graph as d2
+from deconvolution.d2graph import d2_graph as d2
def parse_arguments():
diff --git a/setup.py b/setup.py
index e69de29..926e3d9 100644
--- a/setup.py
+++ b/setup.py
@@ -0,0 +1,10 @@
+from distutils.core import setup
+
+
+setup(
+ name='10X-deconvolve',
+ version='0.1dev',
+ packages=['deconvolution.d2graph', 'deconvolution.dgraph', 'deconvolution.main'],
+ license='AGPL V3',
+ long_description=open('README.md').read(),
+)
diff --git a/tests/Index_test.py b/tests/Index_test.py
index 393d37a..9b88088 100644
--- a/tests/Index_test.py
+++ b/tests/Index_test.py
@@ -1,10 +1,10 @@
import unittest
-
from random import randint
-from dgraph.FixedDGIndex import FixedDGIndex
-from dgraph.VariableDGIndex import VariableDGIndex
-from dgraph.d_graph import Dgraph
-from dgraph.graph_manipulator import generate_d_graph_chain
+
+from deconvolution.dgraph.FixedDGIndex import FixedDGIndex
+from deconvolution.dgraph.VariableDGIndex import VariableDGIndex
+from deconvolution.dgraph.d_graph import Dgraph
+from deconvolution.dgraph.graph_manipulator import generate_d_graph_chain
class TestIndex(unittest.TestCase):
diff --git a/tests/d2_graph_test.py b/tests/d2_graph_test.py
index 7a72e5e..5d78743 100644
--- a/tests/d2_graph_test.py
+++ b/tests/d2_graph_test.py
@@ -3,10 +3,8 @@ import tempfile
import networkx as nx
from scipy.special import comb
-from d2graph.d2_graph import D2Graph
-from dgraph import graph_manipulator as gm
-
-from d_graph_data import complete_graph
+from deconvolution.d2graph.d2_graph import D2Graph
+from deconvolution.dgraph import graph_manipulator as gm
class TestD2Graph(unittest.TestCase):
diff --git a/tests/d_graph_test.py b/tests/d_graph_test.py
index ddbc259..16b746c 100644
--- a/tests/d_graph_test.py
+++ b/tests/d_graph_test.py
@@ -1,8 +1,8 @@
import unittest
from d_graph_data import unit_d_graph
-from dgraph.d_graph import Dgraph
-from dgraph import graph_manipulator as gm
+from deconvolution.dgraph.d_graph import Dgraph
+from deconvolution.dgraph import graph_manipulator as gm
class TestDGraph(unittest.TestCase):
diff --git a/tests/graph_manipulation_test.py b/tests/graph_manipulation_test.py
index 4ff4a38..da597dd 100644
--- a/tests/graph_manipulation_test.py
+++ b/tests/graph_manipulation_test.py
@@ -1,6 +1,6 @@
import unittest
-from dgraph import graph_manipulator as gm
+from deconvolution.dgraph import graph_manipulator as gm
class TestGraphManipulation(unittest.TestCase):
--
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