Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4/mira4.py @ 4:df86ed992a1b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded preview 4, lots of work on mapping
author peterjc
date Fri, 11 Oct 2013 04:28:45 -0400
parents 32f693f6e741
children ffefb87bd414
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
1 #!/usr/bin/env python
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
2 """A simple wrapper script to call MIRA and collect its output.
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
3 """
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
4 import os
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
5 import sys
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
6 import subprocess
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
7 import shutil
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
8 import time
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
9
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
10 WRAPPER_VER = "0.0.1" #Keep in sync with the XML file
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
11
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
12 def stop_err(msg, err=1):
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
13 sys.stderr.write(msg+"\n")
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
14 sys.exit(err)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
15
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
16
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
17 def get_version(mira_binary):
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
18 """Run MIRA to find its version number"""
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
19 # At the commend line I would use: mira -v | head -n 1
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
20 # however there is some pipe error when doing that here.
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
21 cmd = [mira_binary, "-v"]
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
22 try:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
23 child = subprocess.Popen(cmd,
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
24 stdout=subprocess.PIPE,
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
25 stderr=subprocess.STDOUT)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
26 except Exception, err:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
27 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
28 sys.exit(1)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
29 ver, tmp = child.communicate()
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
30 del child
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
31 return ver.split("\n", 1)[0]
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
32
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
33
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
34 os.environ["PATH"] = "/mnt/galaxy/downloads/mira_4.0rc3_linux-gnu_x86_64_static/bin/:%s" % os.environ["PATH"]
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
35 mira_binary = "mira"
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
36 mira_ver = get_version(mira_binary)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
37 if not mira_ver.strip().startswith("4.0"):
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
38 stop_err("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
39 if "-v" in sys.argv:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
40 print "MIRA wrapper version %s," % WRAPPER_VER
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
41 print mira_ver
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
42 sys.exit(0)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
43
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
44
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
45 def log_manifest(manifest):
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
46 """Write the manifest file to stderr."""
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
47 sys.stderr.write("\n%s\nManifest file\n%s\n" % ("="*60, "="*60))
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
48 with open(manifest) as h:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
49 for line in h:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
50 sys.stderr.write(line)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
51 sys.stderr.write("\n%s\nEnd of manifest\n%s\n" % ("="*60, "="*60))
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
52
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
53
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
54 def collect_output(temp, name, handle):
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
55 n3 = (temp, name, name, name)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
56 f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
57 if not os.path.isdir(f):
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
58 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
59 stop_err("Missing output folder")
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
60 if not os.listdir(f):
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
61 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
62 stop_err("Empty output folder")
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
63 missing = []
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
64
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
65 old_maf = "%s/%s_out.maf" % (f, name)
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
66 if not os.path.isfile(old_maf):
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
67 #Triggered extractLargeContigs.sh?
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
68 old_maf = "%s/%s_LargeContigs_out.maf" % (f, name)
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
69
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
70 #De novo or single strain mapping,
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
71 old_fasta = "%s/%s_out.unpadded.fasta" % (f, name)
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
72 if not os.path.isfile(old_fasta):
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
73 #Mapping (currently StrainX versus reference)
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
74 old_fasta = "%s/%s_out_StrainX.unpadded.fasta" % (f, name)
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
75 if not os.path.isfile(old_fasta):
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
76 #Triggered extractLargeContigs.sh?
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
77 old_fasta = "%s/%s_LargeContigs_out.fasta" % (f, name)
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
78
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
79 missing = False
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
80 for old, new in [(old_maf, out_maf),
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
81 (old_fasta, out_fasta)]:
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
82 if not os.path.isfile(old):
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
83 missing = True
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
84 else:
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
85 handle.write("Capturing %s\n" % old)
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
86 shutil.move(old, new)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
87 if missing:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
88 log_manifest(manifest)
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
89 sys.stderr.write("Contents of %r:\n" % f)
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
90 for filename in sorted(os.listdir(f)):
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
91 sys.stderr.write("%s\n" % filename)
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
92
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
93 def clean_up(temp, name):
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
94 folder = "%s/%s_assembly" % (temp, name)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
95 if os.path.isdir(folder):
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
96 shutil.rmtree(folder)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
97
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
98 #TODO - Run MIRA in /tmp or a configurable directory?
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
99 #Currently Galaxy puts us somewhere safe like:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
100 #/opt/galaxy-dist/database/job_working_directory/846/
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
101 temp = "."
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
102 #name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8]
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
103 name = "MIRA"
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
104 manifest, out_maf, out_fasta, out_log = sys.argv[1:5]
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
105
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
106 start_time = time.time()
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
107 #cmd_list =sys.argv[8:]
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
108 cmd_list = [mira_binary, manifest]
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
109 cmd = " ".join(cmd_list)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
110
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
111 assert os.path.isdir(temp)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
112 d = "%s_assembly" % name
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
113 assert not os.path.isdir(d), "Path %s already exists" % d
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
114 try:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
115 #Check path access
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
116 os.mkdir(d)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
117 except Exception, err:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
118 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
119 sys.stderr.write("Error making directory %s\n%s" % (d, err))
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
120 sys.exit(1)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
121
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
122 #print os.path.abspath(".")
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
123 #print cmd
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
124
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
125 handle = open(out_log, "w")
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
126 handle.write("======================== MIRA manifest (instructions) ========================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
127 m = open(manifest, "rU")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
128 for line in m:
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
129 handle.write(line)
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
130 m.close()
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
131 del m
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
132 handle.write("\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
133 handle.write("============================ Starting MIRA now ===============================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
134 handle.flush()
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
135 try:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
136 #Run MIRA
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
137 child = subprocess.Popen(cmd_list,
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
138 stdout=handle,
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
139 stderr=subprocess.STDOUT)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
140 except Exception, err:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
141 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
142 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
143 #TODO - call clean up?
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
144 handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
145 handle.close()
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
146 sys.exit(1)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
147 #Use .communicate as can get deadlocks with .wait(),
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
148 stdout, stderr = child.communicate()
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
149 assert not stdout and not stderr #Should be empty as sent to handle
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
150 run_time = time.time() - start_time
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
151 return_code = child.returncode
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
152 handle.write("\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
153 handle.write("============================ MIRA has finished ===============================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
154 handle.write("MIRA took %0.2f hours\n" % (run_time / 3600.0))
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
155 print "MIRA took %0.2f hours" % (run_time / 3600.0)
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
156 if return_code:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
157 handle.write("Return error code %i from command:\n" % return_code)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
158 handle.write(cmd + "\n")
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
159 handle.close()
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
160 clean_up(temp, name)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
161 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
162 stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
163 return_code)
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
164 handle.flush()
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
165
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
166 if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"):
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
167 handle.write("\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
168 handle.write("====================== Extract Large Contigs failed ==========================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
169 e = open("MIRA_assembly/MIRA_d_results/ec.log", "rU")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
170 for line in e:
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
171 handle.write(line)
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
172 e.close()
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
173 handle.write("============================ (end of ec.log) =================================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
174 handle.flush()
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
175
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
176 #print "Collecting output..."
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
177 collect_output(temp, name, handle)
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
178
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
179 if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"):
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
180 #Treat as an error, but doing this AFTER collect_output
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
181 sys.stderr.write("Extract Large Contigs failed\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
182 handle.write("Extract Large Contigs failed\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
183 handle.close()
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
184 sys.exit(1)
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
185
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
186 #print "Cleaning up..."
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
187 clean_up(temp, name)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
188
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
189 handle.close()
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
190 print("Done")