diff --git a/Tests/test_orthofinder.py b/Tests/test_orthofinder.py
index 2be830c9e0d7e13536d10c7378ea62714105cb0c..4c7264e0521c6df5f3879e75adf7cd70aa50b050 100755
--- a/Tests/test_orthofinder.py
+++ b/Tests/test_orthofinder.py
@@ -34,7 +34,7 @@ exampleBlastDir = baseDir + "Input/SmallExampleDataset_ExampleBlastDir/"
goldResultsDir_smallExample = baseDir + "ExpectedOutput/SmallExampleDataset/"
goldPrepareBlastDir = baseDir + "ExpectedOutput/SmallExampleDataset_PreparedForBlast/"
-version = "1.0.4"
+version = "1.0.5"
requiredBlastVersion = "2.2.28+"
citation = """When publishing work that uses OrthoFinder please cite:
@@ -50,10 +50,9 @@ expectedHelp="""OrthoFinder version %s Copyright (C) 2014 David Emms
Simple Usage
------------
-python orthofinder.py -f fasta_directory [-t number_of_blast_threads] [-a number_of_orthofinder_threads]
+python orthofinder.py -f fasta_directory [-t number_of_blast_threads]
Infers orthogroups for the proteomes contained in fasta_directory running
- number_of_blast_threads in parallel for the BLAST searches and subsequently running
- number_of_orthofinder_threads in parallel for the OrthoFinder algorithm.
+ number_of_blast_threads in parallel for the BLAST searches and tree inference.
Advanced Usage
--------------
@@ -91,14 +90,14 @@ Arguments
Running the OrthoFinder algorithm with a number of threads simultaneously increases the RAM
requirements proportionally so be aware of the amount of RAM you have available (and see README file).
Additionally, as the algorithm implementation is very fast, file reading is likely to be the
- limiting factor above about 5-10 threads and additional threads may have little effect other than
+ limiting factor above about 5-10 threads and additional threads may have little effect other than to
increase RAM requirements. [Default is 1]
-g, --groups
Only infer orthogroups, do not infer gene trees of orthologues.
-I inflation_parameter, --inflation inflation_parameter
- Specify a non-default inflation parameter for MCL. [Default is 1.5]
+ Specify a non-default inflation parameter for MCL. Not recommended. [Default is 1.5]
-x speciesInfoFilename, --orthoxml speciesInfoFilename
Output the orthogroups in the orthoxml format using the information in speciesInfoFilename.
diff --git a/orthofinder/orthofinder.py b/orthofinder/orthofinder.py
index d47d17f677b159013c4ab29071af7cecc93b314c..7bbc206f33f896eae5158b53e42f67c308fe00a5 100755
--- a/orthofinder/orthofinder.py
+++ b/orthofinder/orthofinder.py
@@ -733,10 +733,9 @@ def CanRunMCL():
def PrintHelp():
print("Simple Usage")
print("------------")
- print("python orthofinder.py -f fasta_directory [-t number_of_blast_threads] [-a number_of_orthofinder_threads]")
+ print("python orthofinder.py -f fasta_directory [-t number_of_blast_threads]")
print(" Infers orthogroups for the proteomes contained in fasta_directory running")
- print(" number_of_blast_threads in parallel for the BLAST searches and subsequently running")
- print(" number_of_orthofinder_threads in parallel for the OrthoFinder algorithm.")
+ print(" number_of_blast_threads in parallel for the BLAST searches and tree inference.")
print("")
print("Advanced Usage")
print("--------------")
@@ -774,14 +773,14 @@ def PrintHelp():
Running the OrthoFinder algorithm with a number of threads simultaneously increases the RAM
requirements proportionally so be aware of the amount of RAM you have available (and see README file).
Additionally, as the algorithm implementation is very fast, file reading is likely to be the
- limiting factor above about 5-10 threads and additional threads may have little effect other than
+ limiting factor above about 5-10 threads and additional threads may have little effect other than to
increase RAM requirements. [Default is %d]\n""" % util.nAlgDefault)
print("""-g, --groups
Only infer orthogroups, do not infer gene trees of orthologues.\n""")
print("""-I inflation_parameter, --inflation inflation_parameter
- Specify a non-default inflation parameter for MCL. [Default is %0.1f]\n""" % mclInflation)
+ Specify a non-default inflation parameter for MCL. Not recommended. [Default is %0.1f]\n""" % mclInflation)
print("""-x speciesInfoFilename, --orthoxml speciesInfoFilename
Output the orthogroups in the orthoxml format using the information in speciesInfoFilename.\n""")
diff --git a/orthofinder/scripts/get_orthologues.py b/orthofinder/scripts/get_orthologues.py
index 6902a83bf38b374e0ea29137617a2d190ebb3a5a..e813f48380b3027e60383f5cdc2cb5502f8eb174 100755
--- a/orthofinder/scripts/get_orthologues.py
+++ b/orthofinder/scripts/get_orthologues.py
@@ -28,6 +28,7 @@
import os
import sys
import glob
+import time
import shutil
import subprocess
import numpy as np
@@ -524,15 +525,18 @@ def GetResultsFilesString(rootedSpeciesTreeFN):
st += "Species-by-species orthologues directory:\n %s\n\n" % resultsDir
return st
-
def CleanWorkingDir(dendroBlast):
dendroBlast.DeleteBlastMatrices()
dirs = ['Distances/', "matrices_orthologues/", "Trees_ids_arbitraryRoot/"]
for d in dirs:
dFull = dendroBlast.workingDir + d
if os.path.exists(dFull):
- shutil.rmtree(dFull)
-
+ try:
+ shutil.rmtree(dFull)
+ except OSError:
+ time.sleep(1)
+ shutil.rmtree(dFull, True) # shutil / NFS bug - ignore errors, it's less crucial that the files are deleted
+
def GetOrthologues(orthofinderWorkingDir, orthofinderResultsDir, speciesToUse, nSpAll, clustersFilename_pairs, nProcesses):
ogSet = OrthoGroupsSet(orthofinderWorkingDir, speciesToUse, nSpAll, clustersFilename_pairs, idExtractor = util.FirstWordExtractor)
if len(ogSet.speciesToUse) < 4:
diff --git a/orthofinder/scripts/util.py b/orthofinder/scripts/util.py
index 19018e2bbf4e9e79d194534bc2e568289054f104..ae592b188a01299663e9a9d83a1a34b747a92bbd 100644
--- a/orthofinder/scripts/util.py
+++ b/orthofinder/scripts/util.py
@@ -47,7 +47,7 @@ SequencesInfo = namedtuple("SequencesInfo", "nSeqs nSpecies speciesToUse seqStar
FileInfo = namedtuple("FileInfo", "inputDir outputDir graphFilename")
picProtocol = 1
-version = "1.0.4"
+version = "1.0.5"
def PrintNoNewLine(text):
sys.stdout.write(text)