Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4/mira4.py @ 20:aeb3e35f8236 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.0.4 preview, made MAF and BAM output optional
author peterjc
date Tue, 10 Jun 2014 10:11:58 -0400
parents 8487d70e82aa
children 4abe8d59a438
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
18
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
9 import tempfile
20
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
10 from optparse import OptionParser
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
11
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
12 #Do we need any PYTHONPATH magic?
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
13 from mira4_make_bam import make_bam
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
14
20
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
15 WRAPPER_VER = "0.0.4" #Keep in sync with the XML file
0
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 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
18 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
19 sys.exit(err)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
20
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
21
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
22 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
23 """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
24 # 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
25 # 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
26 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
27 try:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
28 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
29 stdout=subprocess.PIPE,
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
30 stderr=subprocess.STDOUT)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
31 except Exception, err:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
32 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
33 sys.exit(1)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
34 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
35 del child
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
36 return ver.split("\n", 1)[0].strip()
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
37
20
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
38 #Parse Command Line
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
39 usage = """Galaxy MIRA4 wrapper script v%s - use as follows:
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
40
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
41 $ python mira4.py ...
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
42
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
43 This will run the MIRA binary and collect its output files as directed.
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
44 """ % WRAPPER_VER
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
45 parser = OptionParser(usage=usage)
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
46 parser.add_option("-m", "--manifest", dest="manifest",
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
47 default=None, metavar="FILE",
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
48 help="MIRA manifest filename")
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
49 parser.add_option("--maf", dest="maf",
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
50 default="-", metavar="FILE",
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
51 help="MIRA MAF output filename")
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
52 parser.add_option("--bam", dest="bam",
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
53 default="-", metavar="FILE",
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
54 help="Unpadded BAM output filename")
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
55 parser.add_option("--fasta", dest="fasta",
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
56 default="-", metavar="FILE",
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
57 help="Unpadded FASTA output filename")
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
58 parser.add_option("--log", dest="log",
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
59 default="-", metavar="FILE",
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
60 help="MIRA logging output filename")
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
61 options, args = parser.parse_args()
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
62 manifest = options.manifest
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
63 out_maf = options.maf
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
64 out_bam = options.bam
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
65 out_fasta = options.fasta
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
66 out_log = options.log
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
67
7
902f01c1084b Uploaded v0.0.1 preview 7, with mirabait wrapper
peterjc
parents: 5
diff changeset
68 try:
902f01c1084b Uploaded v0.0.1 preview 7, with mirabait wrapper
peterjc
parents: 5
diff changeset
69 mira_path = os.environ["MIRA4"]
12
a6a56440567c Uploaded v0.0.2 preview 4, now using MIRA 4.0 (not RC), and sets MIRA4 environment variable during install.
peterjc
parents: 11
diff changeset
70 except KeyError:
7
902f01c1084b Uploaded v0.0.1 preview 7, with mirabait wrapper
peterjc
parents: 5
diff changeset
71 stop_err("Environment variable $MIRA4 not set")
902f01c1084b Uploaded v0.0.1 preview 7, with mirabait wrapper
peterjc
parents: 5
diff changeset
72 mira_binary = os.path.join(mira_path, "mira")
902f01c1084b Uploaded v0.0.1 preview 7, with mirabait wrapper
peterjc
parents: 5
diff changeset
73 if not os.path.isfile(mira_binary):
13
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 12
diff changeset
74 stop_err("Missing mira under $MIRA4, %r\nFolder contained: %s"
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 12
diff changeset
75 % (mira_binary, ", ".join(os.listdir(mira_path))))
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
76 mira_convert = os.path.join(mira_path, "miraconvert")
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
77 if not os.path.isfile(mira_convert):
13
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 12
diff changeset
78 stop_err("Missing miraconvert under $MIRA4, %r\nFolder contained: %s"
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 12
diff changeset
79 % (mira_convert, ", ".join(os.listdir(mira_path))))
7
902f01c1084b Uploaded v0.0.1 preview 7, with mirabait wrapper
peterjc
parents: 5
diff changeset
80
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
81 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
82 if not mira_ver.strip().startswith("4.0"):
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
83 stop_err("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_binary))
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
84 mira_convert_ver = get_version(mira_convert)
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
85 if not mira_convert_ver.strip().startswith("4.0"):
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
86 stop_err("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_convert))
5
ffefb87bd414 Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type)
peterjc
parents: 4
diff changeset
87 if "-v" in sys.argv or "--version" in sys.argv:
ffefb87bd414 Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type)
peterjc
parents: 4
diff changeset
88 print "%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER)
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
89 if mira_ver != mira_convert_ver:
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
90 print "WARNING: miraconvert %s" % mira_convert_ver
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
91 sys.exit(0)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
92
20
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
93 if not manifest:
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
94 stop_err("Manifest is required")
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
95 elif not os.path.isfile(manifest):
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
96 stop_err("Missing input MIRA manifest file: %r" % manifest)
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
97
7
902f01c1084b Uploaded v0.0.1 preview 7, with mirabait wrapper
peterjc
parents: 5
diff changeset
98
11
02350bef2e99 Uploaded v0.0.2 preview 3, correction regression in URL
peterjc
parents: 9
diff changeset
99 try:
02350bef2e99 Uploaded v0.0.2 preview 3, correction regression in URL
peterjc
parents: 9
diff changeset
100 threads = int(os.environ.get("GALAXY_SLOTS", "1"))
02350bef2e99 Uploaded v0.0.2 preview 3, correction regression in URL
peterjc
parents: 9
diff changeset
101 except ValueError:
02350bef2e99 Uploaded v0.0.2 preview 3, correction regression in URL
peterjc
parents: 9
diff changeset
102 threads = 1
02350bef2e99 Uploaded v0.0.2 preview 3, correction regression in URL
peterjc
parents: 9
diff changeset
103 assert 1 <= threads, threads
7
902f01c1084b Uploaded v0.0.1 preview 7, with mirabait wrapper
peterjc
parents: 5
diff changeset
104
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
105
18
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
106 def override_temp(manifest):
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
107 """Override ``-DI:trt=/tmp`` in manifest with environment variable.
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
108
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
109 Currently MIRA 4 does not allow envronment variables like ``$TMP``
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
110 inside the manifest, which is a problem if you need to override
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
111 the default at run time.
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
112
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
113 The tool XML will ``/tmp`` and we replace that here with
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
114 ``tempfile.gettempdir()`` which will respect $TMPDIR, $TEMP, $TMP
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
115 as explained in the Python standard library documentation:
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
116 http://docs.python.org/2/library/tempfile.html#tempfile.tempdir
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
117
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
118 By default MIRA 4 would write its temporary files within the output
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
119 folder, which is a problem if that is a network drive.
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
120 """
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
121 handle = open(manifest, "r")
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
122 text = handle.read()
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
123 handle.close()
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
124
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
125 #At time of writing, this is at the end of a file,
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
126 #but could be followed by a space in future...
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
127 text = text.replace("-DI:trt=/tmp", "-DI:trt=" + tempfile.gettempdir())
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
128
19
8487d70e82aa Uploaded v0.0.3 preview 1, target MIRA v4.0.2
peterjc
parents: 18
diff changeset
129 #Want to try to ensure this gets written to disk before MIRA attempts
8487d70e82aa Uploaded v0.0.3 preview 1, target MIRA v4.0.2
peterjc
parents: 18
diff changeset
130 #to open it - any networked file system may impose a delay...
18
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
131 handle = open(manifest, "w")
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
132 handle.write(text)
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
133 handle.flush()
19
8487d70e82aa Uploaded v0.0.3 preview 1, target MIRA v4.0.2
peterjc
parents: 18
diff changeset
134 os.fsync(handle.fileno())
18
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
135 handle.close()
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
136
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
137
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
138 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
139 """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
140 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
141 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
142 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
143 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
144 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
145
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
146
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
147 def collect_output(temp, name, handle):
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
148 """Moves files to the output filenames (global variables)."""
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
149 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
150 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
151 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
152 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
153 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
154 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
155 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
156 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
157 missing = []
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
158
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
159 old_maf = "%s/%s_out.maf" % (f, name)
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
160 if not os.path.isfile(old_maf):
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
161 #Triggered extractLargeContigs.sh?
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
162 old_maf = "%s/%s_LargeContigs_out.maf" % (f, name)
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
163
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
164 #De novo or single strain mapping,
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
165 old_fasta = "%s/%s_out.unpadded.fasta" % (f, name)
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
166 ref_fasta = "%s/%s_out.padded.fasta" % (f, name)
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
167 if not os.path.isfile(old_fasta):
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
168 #Mapping (StrainX versus reference) or de novo
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
169 old_fasta = "%s/%s_out_StrainX.unpadded.fasta" % (f, name)
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
170 ref_fasta = "%s/%s_out_StrainX.padded.fasta" % (f, name)
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
171 if not os.path.isfile(old_fasta):
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
172 old_fasta = "%s/%s_out_ReferenceStrain.unpadded.fasta" % (f, name)
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
173 ref_fasta = "%s/%s_out_ReferenceStrain.padded.fasta" % (f, name)
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
174
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
175
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
176 missing = False
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
177 for old, new in [(old_maf, out_maf),
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
178 (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
179 if not os.path.isfile(old):
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
180 missing = True
20
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
181 elif not new or new == "-":
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
182 handle.write("Ignoring %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
183 else:
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
184 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
185 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
186 if missing:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
187 log_manifest(manifest)
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
188 sys.stderr.write("Contents of %r:\n" % f)
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
189 for filename in sorted(os.listdir(f)):
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
190 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
191
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
192 #For mapping mode, probably most people would expect a BAM file
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
193 #using the reference FASTA file...
20
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
194 if out_bam and out_bam != "-":
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
195 msg = make_bam(mira_convert, out_maf, ref_fasta, out_bam, handle)
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
196 if msg:
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
197 stop_err(msg)
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
198
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
199 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
200 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
201 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
202 shutil.rmtree(folder)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
203
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
204 #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
205 #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
206 #/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
207 temp = "."
20
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
208
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
209 name = "MIRA"
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
210
18
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
211 override_temp(manifest)
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 13
diff changeset
212
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
213 start_time = time.time()
11
02350bef2e99 Uploaded v0.0.2 preview 3, correction regression in URL
peterjc
parents: 9
diff changeset
214 cmd_list = [mira_binary, "-t", str(threads), manifest]
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
215 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
216
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
217 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
218 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
219 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
220 try:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
221 #Check path access
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
222 os.mkdir(d)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
223 except Exception, err:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
224 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
225 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
226 sys.exit(1)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
227
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
228 #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
229 #print cmd
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
230
20
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
231 if out_log and out_log != "-":
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
232 handle = open(out_log, "w")
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
233 else:
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional
peterjc
parents: 19
diff changeset
234 handle = open(os.devnull, "w")
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
235 handle.write("======================== MIRA manifest (instructions) ========================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
236 m = open(manifest, "rU")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
237 for line in m:
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
238 handle.write(line)
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
239 m.close()
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
240 del m
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
241 handle.write("\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
242 handle.write("============================ Starting MIRA now ===============================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
243 handle.flush()
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
244 try:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
245 #Run MIRA
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
246 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
247 stdout=handle,
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
248 stderr=subprocess.STDOUT)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
249 except Exception, err:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
250 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
251 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
252 #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
253 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
254 handle.close()
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
255 sys.exit(1)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
256 #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
257 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
258 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
259 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
260 return_code = child.returncode
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
261 handle.write("\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
262 handle.write("============================ MIRA has finished ===============================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
263 handle.write("MIRA took %0.2f hours\n" % (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
264 if return_code:
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
265 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
266 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
267 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
268 handle.close()
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
269 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
270 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
271 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
272 return_code)
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
273 handle.flush()
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
274
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
275 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
276 handle.write("\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
277 handle.write("====================== Extract Large Contigs failed ==========================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
278 e = open("MIRA_assembly/MIRA_d_results/ec.log", "rU")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
279 for line in e:
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
280 handle.write(line)
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
281 e.close()
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
282 handle.write("============================ (end of ec.log) =================================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
283 handle.flush()
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
284
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
285 #print "Collecting output..."
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
286 start_time = time.time()
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
287 collect_output(temp, name, handle)
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
288 collect_time = time.time() - start_time
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
289 handle.write("MIRA took %0.2f hours; collecting output %0.2f minutes\n" % (run_time / 3600.0, collect_time / 60.0))
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
290 print("MIRA took %0.2f hours; collecting output %0.2f minutes\n" % (run_time / 3600.0, collect_time / 60.0))
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
291
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
292 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
293 #Treat as an error, but doing this AFTER collect_output
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
294 sys.stderr.write("Extract Large Contigs failed\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
295 handle.write("Extract Large Contigs failed\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
296 handle.close()
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
297 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
298
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
299 #print "Cleaning up..."
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
300 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
301
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
302 handle.write("\nDone\n")
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
303 handle.close()
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
304 print("Done")