mira4_assembler: tools/mira4/mira4.py annotate

annotate tools/mira4/mira4.py @ 21:4abe8d59a438 draft

Uploaded v0.0.4 preview 1; fix getting BAM without MAF

author	peterjc
date	Tue, 28 Oct 2014 08:29:59 -0400
parents	aeb3e35f8236
children

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")
21 4abe8d59a438 Uploaded v0.0.4 preview 1; fix getting BAM without MAF peterjc parents: 20 diff changeset	61 parser.add_option("-v", "--version", dest="version",
4abe8d59a438 Uploaded v0.0.4 preview 1; fix getting BAM without MAF peterjc parents: 20 diff changeset	62 default=False, action="store_true",
4abe8d59a438 Uploaded v0.0.4 preview 1; fix getting BAM without MAF peterjc parents: 20 diff changeset	63 help="Show version and quit")
20 aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	64 options, args = parser.parse_args()
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	65 manifest = options.manifest
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	66 out_maf = options.maf
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	67 out_bam = options.bam
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	68 out_fasta = options.fasta
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	69 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	70
7 902f01c1084b Uploaded v0.0.1 preview 7, with mirabait wrapper peterjc parents: 5 diff changeset	71 try:
902f01c1084b Uploaded v0.0.1 preview 7, with mirabait wrapper peterjc parents: 5 diff changeset	72 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	73 except KeyError:
7 902f01c1084b Uploaded v0.0.1 preview 7, with mirabait wrapper peterjc parents: 5 diff changeset	74 stop_err("Environment variable $MIRA4 not set")
902f01c1084b Uploaded v0.0.1 preview 7, with mirabait wrapper peterjc parents: 5 diff changeset	75 mira_binary = os.path.join(mira_path, "mira")
902f01c1084b Uploaded v0.0.1 preview 7, with mirabait wrapper peterjc parents: 5 diff changeset	76 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	77 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	78 % (mira_binary, ", ".join(os.listdir(mira_path))))
9 302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	79 mira_convert = os.path.join(mira_path, "miraconvert")
302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	80 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	81 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	82 % (mira_convert, ", ".join(os.listdir(mira_path))))
7 902f01c1084b Uploaded v0.0.1 preview 7, with mirabait wrapper peterjc parents: 5 diff changeset	83
0 32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	84 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	85 if not mira_ver.strip().startswith("4.0"):
9 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_binary))
302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	87 mira_convert_ver = get_version(mira_convert)
302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	88 if not mira_convert_ver.strip().startswith("4.0"):
302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	89 stop_err("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_convert))
21 4abe8d59a438 Uploaded v0.0.4 preview 1; fix getting BAM without MAF peterjc parents: 20 diff changeset	90 if options.version:
5 ffefb87bd414 Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type) peterjc parents: 4 diff changeset	91 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	92 if mira_ver != mira_convert_ver:
302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	93 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	94 sys.exit(0)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	95
20 aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	96 if not manifest:
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	97 stop_err("Manifest is required")
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	98 elif not os.path.isfile(manifest):
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	99 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	100
7 902f01c1084b Uploaded v0.0.1 preview 7, with mirabait wrapper peterjc parents: 5 diff changeset	101
11 02350bef2e99 Uploaded v0.0.2 preview 3, correction regression in URL peterjc parents: 9 diff changeset	102 try:
02350bef2e99 Uploaded v0.0.2 preview 3, correction regression in URL peterjc parents: 9 diff changeset	103 threads = int(os.environ.get("GALAXY_SLOTS", "1"))
02350bef2e99 Uploaded v0.0.2 preview 3, correction regression in URL peterjc parents: 9 diff changeset	104 except ValueError:
02350bef2e99 Uploaded v0.0.2 preview 3, correction regression in URL peterjc parents: 9 diff changeset	105 threads = 1
02350bef2e99 Uploaded v0.0.2 preview 3, correction regression in URL peterjc parents: 9 diff changeset	106 assert 1 <= threads, threads
7 902f01c1084b Uploaded v0.0.1 preview 7, with mirabait wrapper peterjc parents: 5 diff changeset	107
0 32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	108
18 381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable peterjc parents: 13 diff changeset	109 def override_temp(manifest):
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable peterjc parents: 13 diff changeset	110 """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	111
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable peterjc parents: 13 diff changeset	112 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	113 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	114 the default at run time.
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable peterjc parents: 13 diff changeset	115
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable peterjc parents: 13 diff changeset	116 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	117 ``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	118 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	119 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	120
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable peterjc parents: 13 diff changeset	121 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	122 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	123 """
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable peterjc parents: 13 diff changeset	124 handle = open(manifest, "r")
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable peterjc parents: 13 diff changeset	125 text = handle.read()
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable peterjc parents: 13 diff changeset	126 handle.close()
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable peterjc parents: 13 diff changeset	127
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable peterjc parents: 13 diff changeset	128 #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	129 #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	130 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	131
19 8487d70e82aa Uploaded v0.0.3 preview 1, target MIRA v4.0.2 peterjc parents: 18 diff changeset	132 #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	133 #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	134 handle = open(manifest, "w")
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable peterjc parents: 13 diff changeset	135 handle.write(text)
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable peterjc parents: 13 diff changeset	136 handle.flush()
19 8487d70e82aa Uploaded v0.0.3 preview 1, target MIRA v4.0.2 peterjc parents: 18 diff changeset	137 os.fsync(handle.fileno())
18 381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable peterjc parents: 13 diff changeset	138 handle.close()
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable peterjc parents: 13 diff changeset	139
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable peterjc parents: 13 diff changeset	140
0 32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	141 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	142 """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	143 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	144 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	145 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	146 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	147 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	148
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	149
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	150 def collect_output(temp, name, handle):
9 302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	151 """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	152 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	153 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	154 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	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("Missing output folder")
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	157 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	158 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	159 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	160 missing = []
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	161
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	162 old_maf = "%s/%s_out.maf" % (f, name)
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	163 if not os.path.isfile(old_maf):
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	164 #Triggered extractLargeContigs.sh?
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	165 old_maf = "%s/%s_LargeContigs_out.maf" % (f, name)
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	166
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	167 #De novo or single strain mapping,
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	168 old_fasta = "%s/%s_out.unpadded.fasta" % (f, name)
9 302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	169 ref_fasta = "%s/%s_out.padded.fasta" % (f, name)
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	170 if not os.path.isfile(old_fasta):
9 302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	171 #Mapping (StrainX versus reference) or de novo
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	172 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	173 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	174 if not os.path.isfile(old_fasta):
9 302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	175 old_fasta = "%s/%s_out_ReferenceStrain.unpadded.fasta" % (f, name)
302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	176 ref_fasta = "%s/%s_out_ReferenceStrain.padded.fasta" % (f, name)
302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	177
4 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 missing = False
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	180 for old, new in [(old_maf, out_maf),
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	181 (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	182 if not os.path.isfile(old):
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	183 missing = True
20 aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	184 elif not new or new == "-":
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	185 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	186 else:
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	187 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	188 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	189 if missing:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	190 log_manifest(manifest)
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	191 sys.stderr.write("Contents of %r:\n" % f)
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	192 for filename in sorted(os.listdir(f)):
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	193 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	194
9 302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	195 #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	196 #using the reference FASTA file...
20 aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	197 if out_bam and out_bam != "-":
21 4abe8d59a438 Uploaded v0.0.4 preview 1; fix getting BAM without MAF peterjc parents: 20 diff changeset	198 if out_maf and out_maf != "-":
4abe8d59a438 Uploaded v0.0.4 preview 1; fix getting BAM without MAF peterjc parents: 20 diff changeset	199 msg = make_bam(mira_convert, out_maf, ref_fasta, out_bam, handle)
4abe8d59a438 Uploaded v0.0.4 preview 1; fix getting BAM without MAF peterjc parents: 20 diff changeset	200 else:
4abe8d59a438 Uploaded v0.0.4 preview 1; fix getting BAM without MAF peterjc parents: 20 diff changeset	201 #Not collecting the MAF file, use original location
4abe8d59a438 Uploaded v0.0.4 preview 1; fix getting BAM without MAF peterjc parents: 20 diff changeset	202 msg = make_bam(mira_convert, old_maf, ref_fasta, out_bam, handle)
20 aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	203 if msg:
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	204 stop_err(msg)
9 302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	205
0 32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	206 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	207 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	208 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	209 shutil.rmtree(folder)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	210
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	211 #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	212 #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	213 #/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	214 temp = "."
20 aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	215
0 32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	216 name = "MIRA"
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	217
18 381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable peterjc parents: 13 diff changeset	218 override_temp(manifest)
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable peterjc parents: 13 diff changeset	219
0 32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	220 start_time = time.time()
11 02350bef2e99 Uploaded v0.0.2 preview 3, correction regression in URL peterjc parents: 9 diff changeset	221 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	222 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	223
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	224 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	225 d = "%s_assembly" % name
21 4abe8d59a438 Uploaded v0.0.4 preview 1; fix getting BAM without MAF peterjc parents: 20 diff changeset	226 #This can fail on my development machine if stale folders exist
4abe8d59a438 Uploaded v0.0.4 preview 1; fix getting BAM without MAF peterjc parents: 20 diff changeset	227 #under Galaxy's .../database/job_working_directory/ tree:
4abe8d59a438 Uploaded v0.0.4 preview 1; fix getting BAM without MAF peterjc parents: 20 diff changeset	228 assert not os.path.isdir(d), "Path %r already exists:\n%s" % (d, os.path.abspath(d))
0 32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	229 try:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	230 #Check path access
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	231 os.mkdir(d)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	232 except Exception, err:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	233 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	234 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	235 sys.exit(1)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	236
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	237 #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	238 #print cmd
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	239
20 aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	240 if out_log and out_log != "-":
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	241 handle = open(out_log, "w")
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	242 else:
aeb3e35f8236 Uploaded v0.0.4 preview, made MAF and BAM output optional peterjc parents: 19 diff changeset	243 handle = open(os.devnull, "w")
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	244 handle.write("======================== MIRA manifest (instructions) ========================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	245 m = open(manifest, "rU")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	246 for line in m:
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	247 handle.write(line)
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	248 m.close()
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	249 del m
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	250 handle.write("\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	251 handle.write("============================ Starting MIRA now ===============================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	252 handle.flush()
0 32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	253 try:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	254 #Run MIRA
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	255 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	256 stdout=handle,
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	257 stderr=subprocess.STDOUT)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	258 except Exception, err:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	259 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	260 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	261 #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	262 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	263 handle.close()
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	264 sys.exit(1)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	265 #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	266 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	267 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	268 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	269 return_code = child.returncode
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	270 handle.write("\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	271 handle.write("============================ MIRA has finished ===============================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	272 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	273 if return_code:
9 302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	274 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	275 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	276 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	277 handle.close()
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	278 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	279 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	280 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	281 return_code)
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	282 handle.flush()
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	283
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	284 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	285 handle.write("\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	286 handle.write("====================== Extract Large Contigs failed ==========================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	287 e = open("MIRA_assembly/MIRA_d_results/ec.log", "rU")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	288 for line in e:
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	289 handle.write(line)
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	290 e.close()
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	291 handle.write("============================ (end of ec.log) =================================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	292 handle.flush()
0 32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	293
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	294 #print "Collecting output..."
9 302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	295 start_time = time.time()
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	296 collect_output(temp, name, handle)
9 302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	297 collect_time = time.time() - start_time
302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	298 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	299 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	300
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	301 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	302 #Treat as an error, but doing this AFTER collect_output
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	303 sys.stderr.write("Extract Large Contigs failed\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	304 handle.write("Extract Large Contigs failed\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	305 handle.close()
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	306 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	307
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	308 #print "Cleaning up..."
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	309 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	310
9 302d13490b23 Uploaded v0.0.2 preview 1, BAM output peterjc parents: 7 diff changeset	311 handle.write("\nDone\n")
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	312 handle.close()
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	313 print("Done")

Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4/mira4.py @ 21:4abe8d59a438 draft