Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4/mira4.py @ 0:32f693f6e741 draft

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Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
author peterjc
date Thu, 26 Sep 2013 12:23:42 -0400
parents
children df86ed992a1b
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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
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10 WRAPPER_VER = "0.0.1" #Keep in sync with the XML file
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11
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12 def stop_err(msg, err=1):
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13 sys.stderr.write(msg+"\n")
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14 sys.exit(err)
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15
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16
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17 def get_version(mira_binary):
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18 """Run MIRA to find its version number"""
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19 # At the commend line I would use: mira -v | head -n 1
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20 # however there is some pipe error when doing that here.
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21 cmd = [mira_binary, "-v"]
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22 try:
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23 child = subprocess.Popen(cmd,
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24 stdout=subprocess.PIPE,
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25 stderr=subprocess.STDOUT)
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26 except Exception, err:
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27 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
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28 sys.exit(1)
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29 ver, tmp = child.communicate()
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30 del child
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31 return ver.split("\n", 1)[0]
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32
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33
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34 os.environ["PATH"] = "/mnt/galaxy/downloads/mira_4.0rc2_linux-gnu_x86_64_static/bin/:%s" % os.environ["PATH"]
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35 mira_binary = "mira"
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36 mira_ver = get_version(mira_binary)
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37 if not mira_ver.strip().startswith("4.0"):
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38 stop_err("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver)
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39 if "-v" in sys.argv:
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40 print "MIRA wrapper version %s," % WRAPPER_VER
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41 print mira_ver
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42 sys.exit(0)
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43
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44
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45 def log_manifest(manifest):
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46 """Write the manifest file to stderr."""
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47 sys.stderr.write("\n%s\nManifest file\n%s\n" % ("="*60, "="*60))
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48 with open(manifest) as h:
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49 for line in h:
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50 sys.stderr.write(line)
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51 sys.stderr.write("\n%s\nEnd of manifest\n%s\n" % ("="*60, "="*60))
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52
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53
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54 def massage_symlinks(manifest):
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55 """Create FASTQ aliases and edit the manifest to use them.
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56
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57 Short term measure for MIRA 4.0RC2 which depends on data file
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58 extensions to decide the file format, and doesn't like *.dat
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59 as used in Galaxy.
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60 """
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61 base = os.path.split(manifest)[0]
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62 with open(manifest) as h:
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63 lines = h.readlines()
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64 f = 0
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65 for i, line in enumerate(lines):
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66 if not line.startswith("data ="):
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67 continue
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68 #Assumes no spaces in filename, would they have to be escaped?
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69 new_line = "data ="
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70 for filename in line[6:].strip().split():
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71 if not filename:
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72 continue
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73 assert os.path.isfile(filename), filename
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74 f += 1
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75 alias = os.path.join(base, "input%i.fastq" % f)
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76 new_line += " " + alias
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77 cmd = "ln -s %s %s" % (filename, alias)
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78 if os.system(cmd):
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79 stop_err("Problem creating FASTQ alias:\n%s" % cmd)
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80 lines[i] = new_line + "\n"
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81 with open(manifest, "w") as h:
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82 for line in lines:
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83 #sys.stderr.write(line)
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84 h.write(line)
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85 return True
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86
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87
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88 def collect_output(temp, name):
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89 n3 = (temp, name, name, name)
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90 f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
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91 if not os.path.isdir(f):
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92 log_manifest(manifest)
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93 stop_err("Missing output folder")
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94 if not os.listdir(f):
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95 log_manifest(manifest)
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96 stop_err("Empty output folder")
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97 missing = []
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98 for old, new in [("%s/%s_out.maf" % (f, name), out_maf),
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99 ("%s/%s_out.unpadded.fasta" % (f, name), out_fasta)]:
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100 if not os.path.isfile(old):
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101 missing.append(os.path.splitext(old)[-1])
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102 else:
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103 shutil.move(old, new)
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104 if missing:
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105 log_manifest(manifest)
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106 sys.stderr.write("Contents of %r: %r\n" % (f, os.listdir(f)))
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107 stop_err("Missing output files: %s" % ", ".join(missing))
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108
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109 def clean_up(temp, name):
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110 folder = "%s/%s_assembly" % (temp, name)
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111 if os.path.isdir(folder):
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112 shutil.rmtree(folder)
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113
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114 #TODO - Run MIRA in /tmp or a configurable directory?
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115 #Currently Galaxy puts us somewhere safe like:
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116 #/opt/galaxy-dist/database/job_working_directory/846/
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117 temp = "."
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118 #name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8]
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119 name = "MIRA"
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120 manifest, out_maf, out_fasta, out_log = sys.argv[1:5]
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121
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122 #Hack until MIRA v4 lets us specify file format explicitly,
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123 massage_symlinks(manifest)
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124
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125 start_time = time.time()
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126 #cmd_list =sys.argv[8:]
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127 cmd_list = [mira_binary, manifest]
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128 cmd = " ".join(cmd_list)
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129
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130 assert os.path.isdir(temp)
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131 d = "%s_assembly" % name
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132 assert not os.path.isdir(d), "Path %s already exists" % d
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133 try:
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134 #Check path access
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135 os.mkdir(d)
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136 except Exception, err:
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137 log_manifest(manifest)
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138 sys.stderr.write("Error making directory %s\n%s" % (d, err))
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139 sys.exit(1)
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140
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141 #print os.path.abspath(".")
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142 #print cmd
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143
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144 handle = open(out_log, "w")
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145 try:
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146 #Run MIRA
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147 child = subprocess.Popen(cmd_list,
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148 stdout=handle,
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149 stderr=subprocess.STDOUT)
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150 except Exception, err:
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151 log_manifest(manifest)
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152 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
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153 #TODO - call clean up?
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154 handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
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155 handle.close()
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156 sys.exit(1)
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157 #Use .communicate as can get deadlocks with .wait(),
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158 stdout, stderr = child.communicate()
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159 assert not stdout and not stderr #Should be empty as sent to handle
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160 run_time = time.time() - start_time
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161 return_code = child.returncode
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162 handle.write("\n\nMIRA took %0.2f minutes\n" % (run_time / 60.0))
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163 print "MIRA took %0.2f minutes" % (run_time / 60.0)
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164 if return_code:
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165 handle.write("Return error code %i from command:\n" % return_code)
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166 handle.write(cmd + "\n")
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167 handle.close()
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168 clean_up(temp, name)
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169 log_manifest(manifest)
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170 stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
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171 return_code)
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172 handle.close()
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173
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174 #print "Collecting output..."
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175 collect_output(temp, name)
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176
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177 #print "Cleaning up..."
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178 clean_up(temp, name)
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179
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180 print "Done"