Mercurial > repos > peterjc > mira_assembler
comparison tools/sr_assembly/mira.py @ 4:117cce3296af
Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
The Galaxy wrapper will no longer work with MIRA v3.2.x - if you are still using the old version of MIRA, please continue to use v0.0.2 of the wrapper.
author | peterjc |
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date | Wed, 21 Dec 2011 11:33:19 -0500 |
parents | 298f5c1d9521 |
children | 3e7eca1f5d04 |
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3:298f5c1d9521 | 4:117cce3296af |
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9 | 9 |
10 def stop_err(msg, err=1): | 10 def stop_err(msg, err=1): |
11 sys.stderr.write(msg+"\n") | 11 sys.stderr.write(msg+"\n") |
12 sys.exit(err) | 12 sys.exit(err) |
13 | 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): | 14 def collect_output(temp, name): |
33 n3 = (temp, name, name, name) | 15 n3 = (temp, name, name, name) |
34 f = "%s/%s_assembly/%s_d_results" % (temp, name, name) | 16 f = "%s/%s_assembly/%s_d_results" % (temp, name, name) |
35 if not os.path.isdir(f): | 17 if not os.path.isdir(f): |
36 stop_err("Missing output folder") | 18 stop_err("Missing output folder") |
37 if not os.listdir(f): | 19 if not os.listdir(f): |
38 stop_err("Empty output folder") | 20 stop_err("Empty output folder") |
21 missing = [] | |
39 for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta), | 22 for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta), |
40 ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual), | 23 ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual), |
41 ("%s/%s_out.wig" % (f, name), out_wig), | 24 ("%s/%s_out.wig" % (f, name), out_wig), |
42 ("%s/%s_out.caf" % (f, name), out_caf), | 25 ("%s/%s_out.caf" % (f, name), out_caf), |
43 ("%s/%s_out.ace" % (f, name), out_ace)]: | 26 ("%s/%s_out.ace" % (f, name), out_ace)]: |
44 if not os.path.isfile(old): | 27 if not os.path.isfile(old): |
45 stop_err("Missing %s output file" % os.path.splitext(old)[-1]) | 28 missing.append(os.path.splitext(old)[-1]) |
46 else: | 29 else: |
47 shutil.move(old, new) | 30 shutil.move(old, new) |
48 tcs_to_tabular("%s/%s_assembly/%s_d_results/%s_out.tcs" % n3, out_tcs) | 31 if missing: |
32 stop_err("Missing output files: %s" % ", ".join(missing)) | |
49 | 33 |
50 def clean_up(temp, name): | 34 def clean_up(temp, name): |
51 folder = "%s/%s_assembly" % (temp, name) | 35 folder = "%s/%s_assembly" % (temp, name) |
52 if os.path.isdir(folder): | 36 if os.path.isdir(folder): |
53 shutil.rmtree(folder) | 37 shutil.rmtree(folder) |
54 | 38 |
55 #TODO - Run MIRA in /tmp or a configurable directory? | 39 #TODO - Run MIRA in /tmp or a configurable directory? |
56 #Currently Galaxy puts us somewhere safe like: | 40 #Currently Galaxy puts us somewhere safe like: |
57 #/opt/galaxy-dist/database/job_working_directory/846/ | 41 #/opt/galaxy-dist/database/job_working_directory/846/ |
58 temp = "." | 42 temp = "." |
59 name, out_fasta, out_qual, out_tcs, out_ace, out_caf, out_wig, out_log = sys.argv[1:9] | 43 name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8] |
60 | 44 |
61 start_time = time.time() | 45 start_time = time.time() |
62 cmd = " ".join(sys.argv[9:]) | 46 cmd_list =sys.argv[8:] |
47 cmd = " ".join(cmd_list) | |
63 | 48 |
64 assert os.path.isdir(temp) | 49 assert os.path.isdir(temp) |
65 d = "%s_assembly" % name | 50 d = "%s_assembly" % name |
66 assert not os.path.isdir(d) | 51 assert not os.path.isdir(d), "Path %s already exists" % d |
67 try: | 52 try: |
68 #Check path access | 53 #Check path access |
69 os.mkdir(d) | 54 os.mkdir(d) |
70 except Exception, err: | 55 except Exception, err: |
71 sys.stderr.write("Error making directory %s\n%s" % (d, err)) | 56 sys.stderr.write("Error making directory %s\n%s" % (d, err)) |
75 #print cmd | 60 #print cmd |
76 | 61 |
77 handle = open(out_log, "w") | 62 handle = open(out_log, "w") |
78 try: | 63 try: |
79 #Run MIRA | 64 #Run MIRA |
80 child = subprocess.Popen(sys.argv[9:], | 65 child = subprocess.Popen(cmd_list, |
81 stdout=handle, | 66 stdout=handle, |
82 stderr=subprocess.STDOUT) | 67 stderr=subprocess.STDOUT) |
83 except Exception, err: | 68 except Exception, err: |
84 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) | 69 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) |
85 #TODO - call clean up? | 70 #TODO - call clean up? |
100 clean_up(temp, name) | 85 clean_up(temp, name) |
101 stop_err("Return error code %i from command:\n%s" % (return_code, cmd), | 86 stop_err("Return error code %i from command:\n%s" % (return_code, cmd), |
102 return_code) | 87 return_code) |
103 handle.close() | 88 handle.close() |
104 | 89 |
90 #print "Collecting output..." | |
105 collect_output(temp, name) | 91 collect_output(temp, name) |
92 | |
93 #print "Cleaning up..." | |
106 clean_up(temp, name) | 94 clean_up(temp, name) |
95 | |
107 print "Done" | 96 print "Done" |