mira4_assembler: tools/mira4/mira4.py annotate

annotate tools/mira4/mira4.py @ 5:ffefb87bd414 draft

Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type)

author	peterjc
date	Tue, 15 Oct 2013 12:07:34 -0400
parents	df86ed992a1b
children	902f01c1084b

rev	line source
0 32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	1 #!/usr/bin/env python
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	2 """A simple wrapper script to call MIRA and collect its output.
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	3 """
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	4 import os
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	5 import sys
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	6 import subprocess
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	7 import shutil
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	8 import time
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	9
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	10 WRAPPER_VER = "0.0.1" #Keep in sync with the XML file
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	11
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	12 def stop_err(msg, err=1):
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	13 sys.stderr.write(msg+"\n")
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	14 sys.exit(err)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	15
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	16
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	17 def get_version(mira_binary):
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	18 """Run MIRA to find its version number"""
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	19 # At the commend line I would use: mira -v \| head -n 1
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	20 # however there is some pipe error when doing that here.
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	21 cmd = [mira_binary, "-v"]
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	22 try:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	23 child = subprocess.Popen(cmd,
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	24 stdout=subprocess.PIPE,
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	25 stderr=subprocess.STDOUT)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	26 except Exception, err:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	27 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	28 sys.exit(1)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	29 ver, tmp = child.communicate()
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	30 del child
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	31 return ver.split("\n", 1)[0]
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	32
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	33
5 ffefb87bd414 Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type) peterjc parents: 4 diff changeset	34 os.environ["PATH"] = "/mnt/galaxy/downloads/mira_4.0rc4_linux-gnu_x86_64_static/bin/:%s" % os.environ["PATH"]
0 32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	35 mira_binary = "mira"
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	36 mira_ver = get_version(mira_binary)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	37 if not mira_ver.strip().startswith("4.0"):
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	38 stop_err("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver)
5 ffefb87bd414 Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type) peterjc parents: 4 diff changeset	39 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	40 print "%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER)
0 32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	41 sys.exit(0)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	42
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	43
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	44 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	45 """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	46 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	47 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	48 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	49 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	50 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	51
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	52
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	53 def collect_output(temp, name, handle):
0 32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	54 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	55 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	56 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	57 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	58 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	59 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	60 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	61 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	62 missing = []
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	63
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	64 old_maf = "%s/%s_out.maf" % (f, name)
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	65 if not os.path.isfile(old_maf):
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	66 #Triggered extractLargeContigs.sh?
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	67 old_maf = "%s/%s_LargeContigs_out.maf" % (f, name)
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	68
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	69 #De novo or single strain mapping,
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	70 old_fasta = "%s/%s_out.unpadded.fasta" % (f, name)
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	71 if not os.path.isfile(old_fasta):
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	72 #Mapping (currently StrainX versus reference)
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	73 old_fasta = "%s/%s_out_StrainX.unpadded.fasta" % (f, name)
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	74 if not os.path.isfile(old_fasta):
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	75 #Triggered extractLargeContigs.sh?
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	76 old_fasta = "%s/%s_LargeContigs_out.fasta" % (f, name)
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	77
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	78 missing = False
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	79 for old, new in [(old_maf, out_maf),
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	80 (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	81 if not os.path.isfile(old):
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	82 missing = True
0 32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	83 else:
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	84 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	85 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	86 if missing:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	87 log_manifest(manifest)
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	88 sys.stderr.write("Contents of %r:\n" % f)
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	89 for filename in sorted(os.listdir(f)):
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	90 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	91
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	92 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	93 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	94 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	95 shutil.rmtree(folder)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	96
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	97 #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	98 #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	99 #/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	100 temp = "."
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	101 #name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8]
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	102 name = "MIRA"
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	103 manifest, out_maf, out_fasta, out_log = sys.argv[1:5]
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	104
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	105 start_time = time.time()
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	106 #cmd_list =sys.argv[8:]
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	107 cmd_list = [mira_binary, manifest]
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	108 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	109
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	110 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	111 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	112 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	113 try:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	114 #Check path access
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	115 os.mkdir(d)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	116 except Exception, err:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	117 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	118 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	119 sys.exit(1)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	120
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	121 #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	122 #print cmd
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	123
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	124 handle = open(out_log, "w")
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	125 handle.write("======================== MIRA manifest (instructions) ========================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	126 m = open(manifest, "rU")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	127 for line in m:
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	128 handle.write(line)
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	129 m.close()
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	130 del m
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	131 handle.write("\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	132 handle.write("============================ Starting MIRA now ===============================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	133 handle.flush()
0 32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	134 try:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	135 #Run MIRA
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	136 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	137 stdout=handle,
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	138 stderr=subprocess.STDOUT)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	139 except Exception, err:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	140 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	141 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	142 #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	143 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	144 handle.close()
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	145 sys.exit(1)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	146 #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	147 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	148 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	149 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	150 return_code = child.returncode
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	151 handle.write("\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	152 handle.write("============================ MIRA has finished ===============================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	153 handle.write("MIRA took %0.2f hours\n" % (run_time / 3600.0))
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	154 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	155 if return_code:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	156 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	157 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	158 handle.close()
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	159 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	160 log_manifest(manifest)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	161 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	162 return_code)
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	163 handle.flush()
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	164
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	165 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	166 handle.write("\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	167 handle.write("====================== Extract Large Contigs failed ==========================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	168 e = open("MIRA_assembly/MIRA_d_results/ec.log", "rU")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	169 for line in e:
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	170 handle.write(line)
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	171 e.close()
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	172 handle.write("============================ (end of ec.log) =================================\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	173 handle.flush()
0 32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	174
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	175 #print "Collecting output..."
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	176 collect_output(temp, name, handle)
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	177
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	178 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	179 #Treat as an error, but doing this AFTER collect_output
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	180 sys.stderr.write("Extract Large Contigs failed\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	181 handle.write("Extract Large Contigs failed\n")
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	182 handle.close()
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	183 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	184
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	185 #print "Cleaning up..."
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency peterjc parents: diff changeset	186 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	187
4 df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	188 handle.close()
df86ed992a1b Uploaded preview 4, lots of work on mapping peterjc parents: 0 diff changeset	189 print("Done")

Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4/mira4.py @ 5:ffefb87bd414 draft