Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4/mira4.py @ 10:79759fdec6cb draft

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Uploaded v0.0.2 preview 2, attempt auto-install for 64 bit Mac OS X.
author peterjc
date Tue, 10 Dec 2013 06:26:19 -0500
parents 302d13490b23
children 02350bef2e99
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0
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1 #!/usr/bin/env python
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2 """A simple wrapper script to call MIRA and collect its output.
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3 """
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4 import os
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5 import sys
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6 import subprocess
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7 import shutil
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8 import time
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9
9
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10 #Do we need any PYTHONPATH magic?
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11 from mira4_make_bam import make_bam
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12
0
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13 WRAPPER_VER = "0.0.1" #Keep in sync with the XML file
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14
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15 def stop_err(msg, err=1):
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16 sys.stderr.write(msg+"\n")
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17 sys.exit(err)
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18
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19
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20 def get_version(mira_binary):
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21 """Run MIRA to find its version number"""
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22 # At the commend line I would use: mira -v | head -n 1
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23 # however there is some pipe error when doing that here.
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24 cmd = [mira_binary, "-v"]
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25 try:
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26 child = subprocess.Popen(cmd,
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27 stdout=subprocess.PIPE,
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28 stderr=subprocess.STDOUT)
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29 except Exception, err:
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30 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
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31 sys.exit(1)
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32 ver, tmp = child.communicate()
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33 del child
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34 return ver.split("\n", 1)[0].strip()
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35
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36
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37 try:
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38 mira_path = os.environ["MIRA4"]
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39 except ImportError:
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40 stop_err("Environment variable $MIRA4 not set")
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41 mira_binary = os.path.join(mira_path, "mira")
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42 if not os.path.isfile(mira_binary):
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43 stop_err("Missing mira under $MIRA4, %r" % mira_binary)
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44 mira_convert = os.path.join(mira_path, "miraconvert")
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45 if not os.path.isfile(mira_convert):
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46 stop_err("Missing miraconvert under $MIRA4, %r" % mira_convert)
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47
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48 mira_ver = get_version(mira_binary)
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49 if not mira_ver.strip().startswith("4.0"):
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50 stop_err("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_binary))
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51 mira_convert_ver = get_version(mira_convert)
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52 if not mira_convert_ver.strip().startswith("4.0"):
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53 stop_err("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_convert))
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54 if "-v" in sys.argv or "--version" in sys.argv:
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55 print "%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER)
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56 if mira_ver != mira_convert_ver:
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57 print "WARNING: miraconvert %s" % mira_convert_ver
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58 sys.exit(0)
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59
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60 def fix_threads(manifest):
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61 """Tweak the manifest to alter the number of threads."""
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62 try:
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63 threads = int(os.environ.get("GALAXY_SLOTS", "1"))
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64 except ValueError:
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65 threads = 1
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66 assert 1 <= threads
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67 if threads == 1:
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68 #Nothing to do...
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69 return
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70
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71 handle = open(manifest)
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72 text = handle.read()
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73 handle.close()
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74
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75 text = text.replace(" -GE:not=1 ", " -GE:not=%i " % threads)
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76
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77 handle = open(manifest, "w")
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78 handle.write(text)
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79 handle.flush()
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80 handle.close()
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81
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82 def log_manifest(manifest):
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83 """Write the manifest file to stderr."""
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84 sys.stderr.write("\n%s\nManifest file\n%s\n" % ("="*60, "="*60))
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85 with open(manifest) as h:
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86 for line in h:
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87 sys.stderr.write(line)
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88 sys.stderr.write("\n%s\nEnd of manifest\n%s\n" % ("="*60, "="*60))
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89
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90
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91 def collect_output(temp, name, handle):
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92 """Moves files to the output filenames (global variables)."""
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93 n3 = (temp, name, name, name)
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94 f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
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95 if not os.path.isdir(f):
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96 log_manifest(manifest)
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97 stop_err("Missing output folder")
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98 if not os.listdir(f):
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99 log_manifest(manifest)
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100 stop_err("Empty output folder")
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101 missing = []
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102
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103 old_maf = "%s/%s_out.maf" % (f, name)
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104 if not os.path.isfile(old_maf):
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105 #Triggered extractLargeContigs.sh?
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106 old_maf = "%s/%s_LargeContigs_out.maf" % (f, name)
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107
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108 #De novo or single strain mapping,
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109 old_fasta = "%s/%s_out.unpadded.fasta" % (f, name)
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110 ref_fasta = "%s/%s_out.padded.fasta" % (f, name)
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111 if not os.path.isfile(old_fasta):
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112 #Mapping (StrainX versus reference) or de novo
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113 old_fasta = "%s/%s_out_StrainX.unpadded.fasta" % (f, name)
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114 ref_fasta = "%s/%s_out_StrainX.padded.fasta" % (f, name)
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115 if not os.path.isfile(old_fasta):
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116 old_fasta = "%s/%s_out_ReferenceStrain.unpadded.fasta" % (f, name)
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117 ref_fasta = "%s/%s_out_ReferenceStrain.padded.fasta" % (f, name)
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118
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119
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120 missing = False
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121 for old, new in [(old_maf, out_maf),
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122 (old_fasta, out_fasta)]:
0
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123 if not os.path.isfile(old):
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124 missing = True
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125 else:
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126 handle.write("Capturing %s\n" % old)
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127 shutil.move(old, new)
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128 if missing:
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129 log_manifest(manifest)
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130 sys.stderr.write("Contents of %r:\n" % f)
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131 for filename in sorted(os.listdir(f)):
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132 sys.stderr.write("%s\n" % filename)
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133
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134 #For mapping mode, probably most people would expect a BAM file
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135 #using the reference FASTA file...
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136 msg = make_bam(mira_convert, out_maf, ref_fasta, out_bam, handle)
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137 if msg:
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138 stop_err(msg)
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139
0
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140 def clean_up(temp, name):
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141 folder = "%s/%s_assembly" % (temp, name)
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142 if os.path.isdir(folder):
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143 shutil.rmtree(folder)
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144
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145 #TODO - Run MIRA in /tmp or a configurable directory?
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146 #Currently Galaxy puts us somewhere safe like:
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147 #/opt/galaxy-dist/database/job_working_directory/846/
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148 temp = "."
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149 #name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8]
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150 name = "MIRA"
9
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151 manifest, out_maf, out_bam, out_fasta, out_log = sys.argv[1:]
0
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152
7
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153 fix_threads(manifest)
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154
0
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155 start_time = time.time()
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156 #cmd_list =sys.argv[8:]
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157 cmd_list = [mira_binary, manifest]
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158 cmd = " ".join(cmd_list)
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159
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160 assert os.path.isdir(temp)
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161 d = "%s_assembly" % name
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162 assert not os.path.isdir(d), "Path %s already exists" % d
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163 try:
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164 #Check path access
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165 os.mkdir(d)
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166 except Exception, err:
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167 log_manifest(manifest)
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168 sys.stderr.write("Error making directory %s\n%s" % (d, err))
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169 sys.exit(1)
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170
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171 #print os.path.abspath(".")
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172 #print cmd
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173
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174 handle = open(out_log, "w")
4
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175 handle.write("======================== MIRA manifest (instructions) ========================\n")
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176 m = open(manifest, "rU")
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177 for line in m:
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178 handle.write(line)
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179 m.close()
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180 del m
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181 handle.write("\n")
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182 handle.write("============================ Starting MIRA now ===============================\n")
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183 handle.flush()
0
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184 try:
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185 #Run MIRA
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186 child = subprocess.Popen(cmd_list,
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187 stdout=handle,
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188 stderr=subprocess.STDOUT)
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189 except Exception, err:
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190 log_manifest(manifest)
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191 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
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192 #TODO - call clean up?
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193 handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
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194 handle.close()
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195 sys.exit(1)
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196 #Use .communicate as can get deadlocks with .wait(),
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197 stdout, stderr = child.communicate()
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198 assert not stdout and not stderr #Should be empty as sent to handle
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199 run_time = time.time() - start_time
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200 return_code = child.returncode
4
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201 handle.write("\n")
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202 handle.write("============================ MIRA has finished ===============================\n")
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203 handle.write("MIRA took %0.2f hours\n" % (run_time / 3600.0))
0
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204 if return_code:
9
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205 print "MIRA took %0.2f hours" % (run_time / 3600.0)
0
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206 handle.write("Return error code %i from command:\n" % return_code)
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207 handle.write(cmd + "\n")
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208 handle.close()
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209 clean_up(temp, name)
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210 log_manifest(manifest)
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211 stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
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212 return_code)
4
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213 handle.flush()
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214
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215 if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"):
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216 handle.write("\n")
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217 handle.write("====================== Extract Large Contigs failed ==========================\n")
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218 e = open("MIRA_assembly/MIRA_d_results/ec.log", "rU")
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219 for line in e:
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220 handle.write(line)
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221 e.close()
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222 handle.write("============================ (end of ec.log) =================================\n")
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223 handle.flush()
0
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224
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225 #print "Collecting output..."
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226 start_time = time.time()
4
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227 collect_output(temp, name, handle)
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228 collect_time = time.time() - start_time
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229 handle.write("MIRA took %0.2f hours; collecting output %0.2f minutes\n" % (run_time / 3600.0, collect_time / 60.0))
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230 print("MIRA took %0.2f hours; collecting output %0.2f minutes\n" % (run_time / 3600.0, collect_time / 60.0))
4
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231
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232 if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"):
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233 #Treat as an error, but doing this AFTER collect_output
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234 sys.stderr.write("Extract Large Contigs failed\n")
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235 handle.write("Extract Large Contigs failed\n")
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236 handle.close()
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237 sys.exit(1)
0
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238
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239 #print "Cleaning up..."
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240 clean_up(temp, name)
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241
9
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242 handle.write("\nDone\n")
4
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243 handle.close()
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244 print("Done")