From 9d2b91766b7d1c12630bba559b8e7f6e3f62e352 Mon Sep 17 00:00:00 2001
From: David Emms <david_emms@hotmail.com>
Date: Tue, 30 Aug 2016 23:34:29 +0100
Subject: [PATCH] Remove scripts directory
---
Tests/test_orthofinder.py | 2 +-
scripts/get_orthologues.py => get_orthologues.py | 2 +-
orthofinder.py | 2 +-
scripts/process_trees.py => process_trees.py | 3 +--
scripts/root_from_duplications.py => root_from_duplications.py | 0
5 files changed, 4 insertions(+), 5 deletions(-)
rename scripts/get_orthologues.py => get_orthologues.py (99%)
rename scripts/process_trees.py => process_trees.py (99%)
rename scripts/root_from_duplications.py => root_from_duplications.py (100%)
diff --git a/Tests/test_orthofinder.py b/Tests/test_orthofinder.py
index a357a68..bdc96f7 100755
--- a/Tests/test_orthofinder.py
+++ b/Tests/test_orthofinder.py
@@ -32,7 +32,7 @@ exampleBlastDir = baseDir + "Input/SmallExampleDataset_ExampleBlastDir/"
goldResultsDir_smallExample = baseDir + "ExpectedOutput/SmallExampleDataset/"
goldPrepareBlastDir = baseDir + "ExpectedOutput/SmallExampleDataset_PreparedForBlast/"
-version = "0.7.1"
+version = "1.0.0"
requiredBlastVersion = "2.2.28+"
citation = """When publishing work that uses OrthoFinder please cite:
diff --git a/scripts/get_orthologues.py b/get_orthologues.py
similarity index 99%
rename from scripts/get_orthologues.py
rename to get_orthologues.py
index f22758c..61b8e1e 100755
--- a/scripts/get_orthologues.py
+++ b/get_orthologues.py
@@ -17,7 +17,7 @@ import itertools
import multiprocessing as mp
import Queue
-sys.path.append(os.path.split(os.path.abspath(__file__))[0] + "/..")
+#sys.path.append(os.path.split(os.path.abspath(__file__))[0] + "/..")
import trees_for_orthogroups as tfo
import orthofinder
import root_from_duplications as rfd
diff --git a/orthofinder.py b/orthofinder.py
index 5fd08b4..b4e72a9 100755
--- a/orthofinder.py
+++ b/orthofinder.py
@@ -51,6 +51,7 @@ import Queue # Y
import warnings # Y
import time # Y
+
version = "1.0.0"
fastaExtensions = {"fa", "faa", "fasta", "fas"}
picProtocol = 1
@@ -1228,7 +1229,6 @@ def AssignIDsToSequences(fastaDirectory, outputDirectory):
return returnFilenames, originalFastaFilenames, idsFilename, speciesFilename, newSpeciesIDs, previousSpeciesIDs
if __name__ == "__main__":
- sys.path.append(os.path.split(os.path.abspath(__file__))[0] + "/scripts")
import get_orthologues
print("\nOrthoFinder version %s Copyright (C) 2014 David Emms\n" % version)
diff --git a/scripts/process_trees.py b/process_trees.py
similarity index 99%
rename from scripts/process_trees.py
rename to process_trees.py
index 94d696b..1c6c337 100644
--- a/scripts/process_trees.py
+++ b/process_trees.py
@@ -10,7 +10,6 @@ from ete2 import Tree
from scipy import sparse
from collections import defaultdict
-sys.path.append(os.path.split(__file__)[0] + "/..")
import orthofinder
def natural_sort_key(s, _nsre=re.compile('([0-9]+)')):
@@ -155,4 +154,4 @@ if __name__ == "__main__":
ogSet = go.OrthoGroupsSet(orthofinderWorkingDir, clustersFilename_pairs, idExtractor = orthofinder.FirstWordExtractor)
get_orthologue_lists(ogSet, resultsDir, dlcparResultsDir, workingDir)
-
\ No newline at end of file
+
diff --git a/scripts/root_from_duplications.py b/root_from_duplications.py
similarity index 100%
rename from scripts/root_from_duplications.py
rename to root_from_duplications.py
--
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