Mercurial > repos > peterjc > mira_assembler
comparison mira_wrapper_v0.0.2.tar.gz/tools/sr_assembly/mira.py @ 1:e53a79816f5f
v0.0.2 - Improve capture of stdout/stderr (should see it as it runs)
author | peterjc |
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date | Thu, 16 Jun 2011 04:44:00 -0400 |
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0:03b240624b5a | 1:e53a79816f5f |
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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 def stop_err(msg, err=1): | |
11 sys.stderr.write(msg+"\n") | |
12 sys.exit(err) | |
13 | |
14 def tcs_to_tabular(old, new): | |
15 in_handle = open(old, "rU") | |
16 out_handle = open(new, "w") | |
17 assert in_handle.readline() == "#TCS V1.0\n" | |
18 assert in_handle.readline() == "#\n" | |
19 assert in_handle.readline() == "# contig name padPos upadPos | B Q | tcov covA covC covG covT cov* | qA qC qG qT q* | S | Tags\n" | |
20 assert in_handle.readline() == "#\n" | |
21 out_handle.write("#%s\n" % "\t".join(["contig", "pasPos", "upadPos", "B", "Q", | |
22 "tcov", "covA", "covC", "covG", "covT", "cov*", | |
23 "qA", "qC", "qG", "qT", "q*", "S", "Tags"])) | |
24 for line in in_handle: | |
25 parts = line.rstrip("\n").split(None,22) | |
26 assert parts[3] == parts[6] == parts[13] == parts[19] == parts[21] == "|" | |
27 wanted = parts[:3] + parts[4:6]+parts[7:13]+parts[14:19]+parts[20:21]+parts[22:] | |
28 out_handle.write("%s\n" % "\t".join(wanted)) | |
29 out_handle.close() | |
30 in_handle.close() | |
31 | |
32 def collect_output(temp, name): | |
33 n3 = (temp, name, name, name) | |
34 f = "%s/%s_assembly/%s_d_results" % (temp, name, name) | |
35 if not os.path.isdir(f): | |
36 stop_err("Missing output folder") | |
37 if not os.listdir(f): | |
38 stop_err("Empty output folder") | |
39 for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta), | |
40 ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual), | |
41 ("%s/%s_out.wig" % (f, name), out_wig), | |
42 ("%s/%s_out.caf" % (f, name), out_caf), | |
43 ("%s/%s_out.ace" % (f, name), out_ace)]: | |
44 if not os.path.isfile(old): | |
45 stop_err("Missing %s output file" % os.path.splitext(old)[-1]) | |
46 else: | |
47 shutil.move(old, new) | |
48 tcs_to_tabular("%s/%s_assembly/%s_d_results/%s_out.tcs" % n3, out_tcs) | |
49 | |
50 def clean_up(temp, name): | |
51 folder = "%s/%s_assembly" % (temp, name) | |
52 if os.path.isdir(folder): | |
53 shutil.rmtree(folder) | |
54 | |
55 #TODO - Run MIRA in /tmp or a configurable directory? | |
56 #Currently Galaxy puts us somewhere safe like: | |
57 #/opt/galaxy-dist/database/job_working_directory/846/ | |
58 temp = "." | |
59 name, out_fasta, out_qual, out_tcs, out_ace, out_caf, out_wig, out_log = sys.argv[1:9] | |
60 | |
61 start_time = time.time() | |
62 cmd = " ".join(sys.argv[9:]) | |
63 | |
64 assert os.path.isdir(temp) | |
65 d = "%s_assembly" % name | |
66 assert not os.path.isdir(d) | |
67 try: | |
68 #Check path access | |
69 os.mkdir(d) | |
70 except Exception, err: | |
71 sys.stderr.write("Error making directory %s\n%s" % (d, err)) | |
72 sys.exit(1) | |
73 | |
74 #print os.path.abspath(".") | |
75 #print cmd | |
76 | |
77 handle = open(out_log, "w") | |
78 try: | |
79 #Run MIRA | |
80 child = subprocess.Popen(sys.argv[9:], | |
81 stdout=handle, | |
82 stderr=subprocess.STDOUT) | |
83 except Exception, err: | |
84 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) | |
85 #TODO - call clean up? | |
86 handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) | |
87 handle.close() | |
88 sys.exit(1) | |
89 #Use .communicate as can get deadlocks with .wait(), | |
90 stdout, stderr = child.communicate() | |
91 assert not stdout and not stderr #Should be empty as sent to handle | |
92 run_time = time.time() - start_time | |
93 return_code = child.returncode | |
94 handle.write("\n\nMIRA took %0.2f minutes\n" % (run_time / 60.0)) | |
95 print "MIRA took %0.2f minutes" % (run_time / 60.0) | |
96 if return_code: | |
97 handle.write("Return error code %i from command:\n" % return_code) | |
98 handle.write(cmd + "\n") | |
99 handle.close() | |
100 clean_up(temp, name) | |
101 stop_err("Return error code %i from command:\n%s" % (return_code, cmd), | |
102 return_code) | |
103 handle.close() | |
104 | |
105 collect_output(temp, name) | |
106 clean_up(temp, name) | |
107 print "Done" |