Mercurial > repos > peterjc > effectivet3

comparison tools/effectiveT3/effectiveT3.py @ 29:35c358aa7801 draft

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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 37d5b47ec23e2cbaa453cc660bb1fcbb10dd34ee-dirty
author peterjc
date Wed, 17 May 2017 11:16:58 -0400
parents af14f755c05b
children 007e86eff414
comparison
equal deleted inserted replaced
28:d6976a4c055b 29:35c358aa7801
19 effective_t3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/") 19 effective_t3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/")
20 effective_t3_jar = os.path.join(effective_t3_dir, "TTSS_GUI-1.0.1.jar") 20 effective_t3_jar = os.path.join(effective_t3_dir, "TTSS_GUI-1.0.1.jar")
21 21
22 if "-v" in sys.argv or "--version" in sys.argv: 22 if "-v" in sys.argv or "--version" in sys.argv:
23 # TODO - Get version of the JAR file dynamically? 23 # TODO - Get version of the JAR file dynamically?
24 print("Wrapper v0.0.17, TTSS_GUI-1.0.1.jar") 24 print("Wrapper v0.0.19, TTSS_GUI-1.0.1.jar")
25 sys.exit(0) 25 sys.exit(0)
26 26
27 if len(sys.argv) != 5: 27 if len(sys.argv) != 5:
28 sys.exit("Require four arguments: model, threshold, input protein FASTA file & output tabular file") 28 sys.exit("Require four arguments: model, threshold, input protein FASTA file & output tabular file")
29 29
72 """Run the command line string via subprocess.""" 72 """Run the command line string via subprocess."""
73 # Avoid using shell=True when we call subprocess to ensure if the Python 73 # Avoid using shell=True when we call subprocess to ensure if the Python
74 # script is killed, so too is the child process. 74 # script is killed, so too is the child process.
75 try: 75 try:
76 child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) 76 child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
77 except Exception, err: 77 except Exception as err:
78 sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) 78 sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
79 # Use .communicate as can get deadlocks with .wait(), 79 # Use .communicate as can get deadlocks with .wait(),
80 stdout, stderr = child.communicate() 80 stdout, stderr = child.communicate()
81 return_code = child.returncode 81 return_code = child.returncode
82 if return_code or stderr.startswith("Exception in thread"): 82 if return_code or stderr.startswith("Exception in thread"):