Mercurial > repos > peterjc > mira4_assembler

comparison tools/mira4_0/mira4_bait.py @ 39:bbf14bb9607b draft default tip

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
author peterjc
date Mon, 03 Jun 2019 13:29:00 -0400
parents cee8f9005e43
children
comparison
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38:cee8f9005e43 39:bbf14bb9607b
16 """Run MIRA to find its version number.""" 16 """Run MIRA to find its version number."""
17 # At the commend line I would use: mira -v | head -n 1 17 # At the commend line I would use: mira -v | head -n 1
18 # however there is some pipe error when doing that here. 18 # however there is some pipe error when doing that here.
19 cmd = [mira_binary, "-v"] 19 cmd = [mira_binary, "-v"]
20 try: 20 try:
21 child = subprocess.Popen(cmd, universal_newlines=True, 21 child = subprocess.Popen(
22 stdout=subprocess.PIPE, 22 cmd,
23 stderr=subprocess.STDOUT) 23 universal_newlines=True,
24 stdout=subprocess.PIPE,
25 stderr=subprocess.STDOUT,
26 )
24 except Exception as err: 27 except Exception as err:
25 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) 28 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
26 sys.exit(1) 29 sys.exit(1)
27 ver, tmp = child.communicate() 30 ver, tmp = child.communicate()
28 del child 31 del child
38 41
39 if "MIRA4" in os.environ: 42 if "MIRA4" in os.environ:
40 mira_path = os.environ["MIRA4"] 43 mira_path = os.environ["MIRA4"]
41 mira_binary = os.path.join(mira_path, "mirabait") 44 mira_binary = os.path.join(mira_path, "mirabait")
42 if not os.path.isfile(mira_binary): 45 if not os.path.isfile(mira_binary):
43 sys.exit("Missing mirabait under $MIRA4, %r\nFolder contained: %s" 46 sys.exit(
44 % (mira_binary, ", ".join(os.listdir(mira_path)))) 47 "Missing mirabait under $MIRA4, %r\nFolder contained: %s"
48 % (mira_binary, ", ".join(os.listdir(mira_path)))
49 )
45 else: 50 else:
46 sys.stderr.write("DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n") 51 sys.stderr.write(
52 "DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n"
53 )
47 mira_path = None 54 mira_path = None
48 mira_binary = "mirabait" 55 mira_binary = "mirabait"
49 56
50 mira_ver = get_version(mira_binary) 57 mira_ver = get_version(mira_binary)
51 if not mira_ver.strip().startswith("4.0"): 58 if not mira_ver.strip().startswith("4.0"):
53 if "-v" in sys.argv or "--version" in sys.argv: 60 if "-v" in sys.argv or "--version" in sys.argv:
54 print("%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER)) 61 print("%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER))
55 sys.exit(0) 62 sys.exit(0)
56 63
57 64
58 format, output_choice, strand_choice, kmer_length, min_occurance, bait_file, in_file, out_file = sys.argv[1:] 65 (
66 format,
67 output_choice,
68 strand_choice,
69 kmer_length,
70 min_occurance,
71 bait_file,
72 in_file,
73 out_file,
74 ) = sys.argv[1:]
59 75
60 if format.startswith("fastq"): 76 if format.startswith("fastq"):
61 format = "fastq" 77 format = "fastq"
62 elif format == "mira": 78 elif format == "mira":
63 format = "maf" 79 format = "maf"
65 sys.exit("Was not expected format %r" % format) 81 sys.exit("Was not expected format %r" % format)
66 82
67 assert out_file.endswith(".dat") 83 assert out_file.endswith(".dat")
68 out_file_stem = out_file[:-4] 84 out_file_stem = out_file[:-4]
69 85
70 cmd_list = [mira_binary, "-f", format, "-t", format, 86 cmd_list = [
71 "-k", kmer_length, "-n", min_occurance, 87 mira_binary,
72 bait_file, in_file, out_file_stem] 88 "-f",
89 format,
90 "-t",
91 format,
92 "-k",
93 kmer_length,
94 "-n",
95 min_occurance,
96 bait_file,
97 in_file,
98 out_file_stem,
99 ]
73 if output_choice == "pos": 100 if output_choice == "pos":
74 pass 101 pass
75 elif output_choice == "neg": 102 elif output_choice == "neg":
76 # Invert the selection... 103 # Invert the selection...
77 cmd_list.insert(1, "-i") 104 cmd_list.insert(1, "-i")
88 cmd = " ".join(cmd_list) 115 cmd = " ".join(cmd_list)
89 # print cmd 116 # print cmd
90 start_time = time.time() 117 start_time = time.time()
91 try: 118 try:
92 # Run MIRA 119 # Run MIRA
93 child = subprocess.Popen(cmd_list, universal_newlines=True, 120 child = subprocess.Popen(
94 stdout=subprocess.PIPE, 121 cmd_list,
95 stderr=subprocess.STDOUT) 122 universal_newlines=True,
123 stdout=subprocess.PIPE,
124 stderr=subprocess.STDOUT,
125 )
96 except Exception as err: 126 except Exception as err:
97 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) 127 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
98 sys.exit(1) 128 sys.exit(1)
99 # Use .communicate as can get deadlocks with .wait(), 129 # Use .communicate as can get deadlocks with .wait(),
100 stdout, stderr = child.communicate() 130 stdout, stderr = child.communicate()
103 return_code = child.returncode 133 return_code = child.returncode
104 print("mirabait took %0.2f minutes" % (run_time / 60.0)) 134 print("mirabait took %0.2f minutes" % (run_time / 60.0))
105 135
106 if return_code: 136 if return_code:
107 sys.stderr.write(stdout) 137 sys.stderr.write(stdout)
108 sys.exit("Return error code %i from command:\n%s" % (return_code, cmd), 138 sys.exit("Return error code %i from command:\n%s" % (return_code, cmd), return_code)
109 return_code)
110 139
111 # Capture output 140 # Capture output
112 out_tmp = out_file_stem + "." + format 141 out_tmp = out_file_stem + "." + format
113 if not os.path.isfile(out_tmp): 142 if not os.path.isfile(out_tmp):
114 sys.stderr.write(stdout) 143 sys.stderr.write(stdout)