Mercurial > repos > peterjc > tmhmm_and_signalp
diff tools/protein_analysis/signalp3.py @ 9:e52220a9ddad draft
Uploaded v0.1.2
Use the new <stdio> settings in the XML wrappers to catch errors.
Obeys SGE style XNSLOTS environment variable for thread count (otherwise default to 4).
| author | peterjc |
|---|---|
| date | Fri, 25 Jan 2013 06:08:31 -0500 |
| parents | 9b45a8743100 |
| children | 99b82a2b1272 |
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--- a/tools/protein_analysis/signalp3.py Mon Jul 30 12:56:54 2012 -0400 +++ b/tools/protein_analysis/signalp3.py Fri Jan 25 06:08:31 2013 -0500 @@ -56,7 +56,8 @@ import sys import os import tempfile -from seq_analysis_utils import stop_err, split_fasta, run_jobs, fasta_iterator +from seq_analysis_utils import stop_err, split_fasta, fasta_iterator +from seq_analysis_utils import run_jobs, thread_count FASTA_CHUNK = 500 MAX_LEN = 6000 #Found by trial and error @@ -78,15 +79,8 @@ if truncate < 0: stop_err("Truncate argument %s is not a positive integer (or zero)" % sys.argv[2]) -try: - num_threads = int(sys.argv[3]) -except: - num_threads = 1 #Default, e.g. used "$NSLOTS" and environment variable not defined -if num_threads < 1: - stop_err("Threads argument %s is not a positive integer" % sys.argv[3]) - +num_threads = thread_count(sys.argv[3], default=4) fasta_file = sys.argv[4] - tabular_file = sys.argv[5] if len(sys.argv) == 8: