From a91b79dfb9e07bdec070a24ac45ae1049176c6a1 Mon Sep 17 00:00:00 2001
From: "Navarro Munoz, Jorge" <jorge.navarromunoz@wur.nl>
Date: Wed, 8 Feb 2017 13:36:49 +0100
Subject: [PATCH] MAFFT: limit number of threads to the --core parameter by
default Use is still able to tweak the mafft_threads parameter to provide a
different number of threads.
---
bigscape.py | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/bigscape.py b/bigscape.py
index c885cb3..2520d17 100644
--- a/bigscape.py
+++ b/bigscape.py
@@ -696,7 +696,7 @@ def CMD_parser():
parser.add_option("-i", "--inputdir", dest="inputdir", default=os.path.dirname(os.path.realpath(__file__)),
help="Input directory of gbk files, if left empty, all gbk files in current and lower directories will be used.")
parser.add_option("-c", "--cores", dest="cores", default=cpu_count(),
- help="Set the amount of cores the script and hmmscan may use (default: use _all_ available cores)")
+ help="Set the amount of cores the script may use (default: use all available cores)")
parser.add_option("-v", "--verbose", dest="verbose", action="store_true", default=False,
help="Prints more detailed information. Toggle to true.")
parser.add_option("--include_disc_nodes", dest="include_disc_nodes", action="store_true", default=False,
@@ -739,8 +739,8 @@ def CMD_parser():
help="alignment method for mafft, if there's a space in the method's name, enclose by quotation marks. default: \"--retree 2\" corresponds to the FFT-NS-2 method")
parser.add_option("--maxiterate", dest="maxit", default=1000,
help="Maxiterate parameter in mafft, default is 1000, corresponds to the FFT-NS-2 method")
- parser.add_option("--mafft_threads", dest="mafft_threads", default=-1,
- help="Set the number of threads in mafft, -1 sets the number of threads as the number of physical cores")
+ parser.add_option("--mafft_threads", dest="mafft_threads", default=0,
+ help="Set the number of threads in mafft, -1 sets the number of threads as the number of physical cores. Default: same as --cores parameter")
parser.add_option("--force_hmmscan", dest="force_hmmscan", action="store_true", default=False,
help="Force domain prediction using hmmscan even if BiG-SCAPE finds processed domtable files (e.g. to use a new version of PFAM).")
@@ -811,6 +811,9 @@ if __name__=="__main__":
print("Please download the latest Pfam-A.hmm file from http://pfam.xfam.org/")
print("Then use hmmpress on it, and use the --pfam_dir parameter to point to the location of the files")
sys.exit()
+
+ if options.mafft_threads == 0:
+ options.mafft_threads = options.cores
verbose = options.verbose
networks_folder = "networks"
--
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