Mercurial > repos > peterjc > mira_assembler

comparison tools/mira_3_4/mira.py @ 8:4266cccbb45a draft

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Uploaded v0.0.7 take 2, fixed path in installation
author peterjc
date Wed, 24 Apr 2013 12:43:17 -0400
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7:4d3f94dfb857 8:4266cccbb45a
1 #!/usr/bin/env python
2 """A simple wrapper script to call MIRA and collect its output.
3 """
4 import os
5 import sys
6 import subprocess
7 import shutil
8 import time
9
10 WRAPPER_VER = "0.0.5" #Keep in sync with the XML file
11
12 def stop_err(msg, err=1):
13 sys.stderr.write(msg+"\n")
14 sys.exit(err)
15
16
17 def get_version():
18 """Run MIRA to find its version number"""
19 # At the commend line I would use: mira -v | head -n 1
20 # however there is some pipe error when doing that here.
21 try:
22 child = subprocess.Popen(["mira", "-v"],
23 stdout=subprocess.PIPE,
24 stderr=subprocess.STDOUT)
25 except Exception, err:
26 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
27 sys.exit(1)
28 ver, tmp = child.communicate()
29 del child
30 return ver.split("\n", 1)[0]
31
32
33 mira_ver = get_version()
34 if "V3.4." not in mira_ver:
35 stop_err("This wrapper is for MIRA V3.4, not %s" % mira_ver)
36 if "-v" in sys.argv:
37 print "MIRA wrapper version %s," % WRAPPER_VER
38 print mira_ver
39 sys.exit(0)
40
41
42 def collect_output(temp, name):
43 n3 = (temp, name, name, name)
44 f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
45 if not os.path.isdir(f):
46 stop_err("Missing output folder")
47 if not os.listdir(f):
48 stop_err("Empty output folder")
49 missing = []
50 for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta),
51 ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual),
52 ("%s/%s_out.wig" % (f, name), out_wig),
53 ("%s/%s_out.caf" % (f, name), out_caf),
54 ("%s/%s_out.ace" % (f, name), out_ace)]:
55 if not os.path.isfile(old):
56 missing.append(os.path.splitext(old)[-1])
57 else:
58 shutil.move(old, new)
59 if missing:
60 stop_err("Missing output files: %s" % ", ".join(missing))
61
62 def clean_up(temp, name):
63 folder = "%s/%s_assembly" % (temp, name)
64 if os.path.isdir(folder):
65 shutil.rmtree(folder)
66
67 #TODO - Run MIRA in /tmp or a configurable directory?
68 #Currently Galaxy puts us somewhere safe like:
69 #/opt/galaxy-dist/database/job_working_directory/846/
70 temp = "."
71 name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8]
72
73 start_time = time.time()
74 cmd_list =sys.argv[8:]
75 cmd = " ".join(cmd_list)
76
77 assert os.path.isdir(temp)
78 d = "%s_assembly" % name
79 assert not os.path.isdir(d), "Path %s already exists" % d
80 try:
81 #Check path access
82 os.mkdir(d)
83 except Exception, err:
84 sys.stderr.write("Error making directory %s\n%s" % (d, err))
85 sys.exit(1)
86
87 #print os.path.abspath(".")
88 #print cmd
89
90 handle = open(out_log, "w")
91 try:
92 #Run MIRA
93 child = subprocess.Popen(cmd_list,
94 stdout=handle,
95 stderr=subprocess.STDOUT)
96 except Exception, err:
97 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
98 #TODO - call clean up?
99 handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
100 handle.close()
101 sys.exit(1)
102 #Use .communicate as can get deadlocks with .wait(),
103 stdout, stderr = child.communicate()
104 assert not stdout and not stderr #Should be empty as sent to handle
105 run_time = time.time() - start_time
106 return_code = child.returncode
107 handle.write("\n\nMIRA took %0.2f minutes\n" % (run_time / 60.0))
108 print "MIRA took %0.2f minutes" % (run_time / 60.0)
109 if return_code:
110 handle.write("Return error code %i from command:\n" % return_code)
111 handle.write(cmd + "\n")
112 handle.close()
113 clean_up(temp, name)
114 stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
115 return_code)
116 handle.close()
117
118 #print "Collecting output..."
119 collect_output(temp, name)
120
121 #print "Cleaning up..."
122 clean_up(temp, name)
123
124 print "Done"