Mercurial > repos > peterjc > mira4_assembler

comparison tools/mira4_0/mira4_bait.py @ 32:56b421d59805 draft

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
author peterjc
date Thu, 18 May 2017 13:36:08 -0400
parents fd95aaef8818
children 0785a6537f3e
comparison
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31:fd95aaef8818 32:56b421d59805
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 """A simple wrapper script to call MIRA4's mirabait and collect its output. 2 """A simple wrapper script to call MIRA4's mirabait and collect its output.
3 """ 3 """
4
5 from __future__ import print_function
6
4 import os 7 import os
8 import shutil
9 import subprocess
5 import sys 10 import sys
6 import subprocess
7 import shutil
8 import time 11 import time
9 12
10 WRAPPER_VER = "0.0.5" #Keep in sync with the XML file 13 WRAPPER_VER = "0.0.10" # Keep in sync with the XML file
11 14
12 15
13 def get_version(mira_binary): 16 def get_version(mira_binary):
14 """Run MIRA to find its version number""" 17 """Run MIRA to find its version number"""
15 # At the commend line I would use: mira -v | head -n 1 18 # At the commend line I would use: mira -v | head -n 1
17 cmd = [mira_binary, "-v"] 20 cmd = [mira_binary, "-v"]
18 try: 21 try:
19 child = subprocess.Popen(cmd, 22 child = subprocess.Popen(cmd,
20 stdout=subprocess.PIPE, 23 stdout=subprocess.PIPE,
21 stderr=subprocess.STDOUT) 24 stderr=subprocess.STDOUT)
22 except Exception, err: 25 except Exception as err:
23 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) 26 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
24 sys.exit(1) 27 sys.exit(1)
25 ver, tmp = child.communicate() 28 ver, tmp = child.communicate()
26 del child 29 del child
27 #Workaround for -v not working in mirabait 4.0RC4 30 # Workaround for -v not working in mirabait 4.0RC4
28 if "invalid option" in ver.split("\n", 1)[0]: 31 if "invalid option" in ver.split("\n", 1)[0]:
29 for line in ver.split("\n", 1): 32 for line in ver.split("\n", 1):
30 if " version " in line: 33 if " version " in line:
31 line = line.split() 34 line = line.split()
32 return line[line.index("version")+1].rstrip(")") 35 return line[line.index("version") + 1].rstrip(")")
33 sys.exit("Could not determine MIRA version:\n%s" % ver) 36 sys.exit("Could not determine MIRA version:\n%s" % ver)
34 return ver.split("\n", 1)[0] 37 return ver.split("\n", 1)[0]
38
35 39
36 try: 40 try:
37 mira_path = os.environ["MIRA4"] 41 mira_path = os.environ["MIRA4"]
38 except KeyError: 42 except KeyError:
39 sys.exit("Environment variable $MIRA4 not set") 43 sys.exit("Environment variable $MIRA4 not set")
43 % (mira_binary, ", ".join(os.listdir(mira_path)))) 47 % (mira_binary, ", ".join(os.listdir(mira_path))))
44 mira_ver = get_version(mira_binary) 48 mira_ver = get_version(mira_binary)
45 if not mira_ver.strip().startswith("4.0"): 49 if not mira_ver.strip().startswith("4.0"):
46 sys.exit("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver) 50 sys.exit("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver)
47 if "-v" in sys.argv or "--version" in sys.argv: 51 if "-v" in sys.argv or "--version" in sys.argv:
48 print "%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER) 52 print("%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER))
49 sys.exit(0) 53 sys.exit(0)
50 54
51 55
52 format, output_choice, strand_choice, kmer_length, min_occurance, bait_file, in_file, out_file = sys.argv[1:] 56 format, output_choice, strand_choice, kmer_length, min_occurance, bait_file, in_file, out_file = sys.argv[1:]
53 57
65 "-k", kmer_length, "-n", min_occurance, 69 "-k", kmer_length, "-n", min_occurance,
66 bait_file, in_file, out_file_stem] 70 bait_file, in_file, out_file_stem]
67 if output_choice == "pos": 71 if output_choice == "pos":
68 pass 72 pass
69 elif output_choice == "neg": 73 elif output_choice == "neg":
70 #Invert the selection... 74 # Invert the selection...
71 cmd_list.insert(1, "-i") 75 cmd_list.insert(1, "-i")
72 else: 76 else:
73 sys.exit("Output choice should be 'pos' or 'neg', not %r" % output_choice) 77 sys.exit("Output choice should be 'pos' or 'neg', not %r" % output_choice)
74 if strand_choice == "both": 78 if strand_choice == "both":
75 pass 79 pass
76 elif strand_choice == "fwd": 80 elif strand_choice == "fwd":
77 #Ingore reverse strand... 81 # Ingore reverse strand...
78 cmd_list.insert(1, "-r") 82 cmd_list.insert(1, "-r")
79 else: 83 else:
80 sys.exit("Strand choice should be 'both' or 'fwd', not %r" % strand_choice) 84 sys.exit("Strand choice should be 'both' or 'fwd', not %r" % strand_choice)
81 85
82 cmd = " ".join(cmd_list) 86 cmd = " ".join(cmd_list)
83 #print cmd 87 # print cmd
84 start_time = time.time() 88 start_time = time.time()
85 try: 89 try:
86 #Run MIRA 90 # Run MIRA
87 child = subprocess.Popen(cmd_list, 91 child = subprocess.Popen(cmd_list,
88 stdout=subprocess.PIPE, 92 stdout=subprocess.PIPE,
89 stderr=subprocess.STDOUT) 93 stderr=subprocess.STDOUT)
90 except Exception, err: 94 except Exception as err:
91 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) 95 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
92 sys.exit(1) 96 sys.exit(1)
93 #Use .communicate as can get deadlocks with .wait(), 97 # Use .communicate as can get deadlocks with .wait(),
94 stdout, stderr = child.communicate() 98 stdout, stderr = child.communicate()
95 assert stderr is None # Due to way we ran with subprocess 99 assert stderr is None # Due to way we ran with subprocess
96 run_time = time.time() - start_time 100 run_time = time.time() - start_time
97 return_code = child.returncode 101 return_code = child.returncode
98 print "mirabait took %0.2f minutes" % (run_time / 60.0) 102 print("mirabait took %0.2f minutes" % (run_time / 60.0))
99 103
100 if return_code: 104 if return_code:
101 sys.stderr.write(stdout) 105 sys.stderr.write(stdout)
102 sys.exit("Return error code %i from command:\n%s" % (return_code, cmd), 106 sys.exit("Return error code %i from command:\n%s" % (return_code, cmd),
103 return_code) 107 return_code)
104 108
105 #Capture output 109 # Capture output
106 out_tmp = out_file_stem + "." + format 110 out_tmp = out_file_stem + "." + format
107 if not os.path.isfile(out_tmp): 111 if not os.path.isfile(out_tmp):
108 sys.stderr.write(stdout) 112 sys.stderr.write(stdout)
109 sys.exit("Missing output file from mirabait: %s" % out_tmp) 113 sys.exit("Missing output file from mirabait: %s" % out_tmp)
110 shutil.move(out_tmp, out_file) 114 shutil.move(out_tmp, out_file)