Mercurial > repos > peterjc > tmhmm_and_signalp

comparison tools/protein_analysis/tmhmm2.py @ 9:e52220a9ddad draft

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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
comparison
equal deleted inserted replaced
8:976a5f2833cd 9:e52220a9ddad
41 when there is no output from tmhmm2, and raise an error. 41 when there is no output from tmhmm2, and raise an error.
42 """ 42 """
43 import sys 43 import sys
44 import os 44 import os
45 import tempfile 45 import tempfile
46 from seq_analysis_utils import stop_err, split_fasta, run_jobs 46 from seq_analysis_utils import stop_err, split_fasta, run_jobs, thread_count
47 47
48 FASTA_CHUNK = 500 48 FASTA_CHUNK = 500
49 49
50 if len(sys.argv) != 4: 50 if len(sys.argv) != 4:
51 stop_err("Require three arguments, number of threads (int), input protein FASTA file & output tabular file") 51 stop_err("Require three arguments, number of threads (int), input protein FASTA file & output tabular file")
52 try: 52
53 num_threads = int(sys.argv[1]) 53 num_threads = thread_count(sys.argv[1], default=4)
54 except:
55 num_threads = 1 #Default, e.g. used "$NSLOTS" and environment variable not defined
56 if num_threads < 1:
57 stop_err("Threads argument %s is not a positive integer" % sys.argv[1])
58 fasta_file = sys.argv[2] 54 fasta_file = sys.argv[2]
59 tabular_file = sys.argv[3] 55 tabular_file = sys.argv[3]
60 56
61 tmp_dir = tempfile.mkdtemp() 57 tmp_dir = tempfile.mkdtemp()
62 58