Mercurial > repos > peterjc > mira_assembler

annotate tools/sr_assembly/mira.py @ 7:4d3f94dfb857 draft

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Uploaded v0.0.6, tell MIRA to use /tmp for temporary files, and ignore long read names (to prevent it aborting).
author peterjc
date Thu, 14 Feb 2013 06:26:32 -0500
parents 3e7eca1f5d04
children
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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
6
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10 WRAPPER_VER = "0.0.5" #Keep in sync with the XML file
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11
0
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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
6
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16
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17 def get_version():
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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 try:
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22 child = subprocess.Popen(["mira", "-v"],
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23 stdout=subprocess.PIPE,
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24 stderr=subprocess.STDOUT)
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25 except Exception, err:
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26 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
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27 sys.exit(1)
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28 ver, tmp = child.communicate()
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29 del child
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30 return ver.split("\n", 1)[0]
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31
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32
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33 mira_ver = get_version()
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34 if "V3.4." not in mira_ver:
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35 stop_err("This wrapper is for MIRA V3.4, not %s" % mira_ver)
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36 if "-v" in sys.argv:
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37 print "MIRA wrapper version %s," % WRAPPER_VER
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38 print mira_ver
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39 sys.exit(0)
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40
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41
0
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42 def collect_output(temp, name):
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43 n3 = (temp, name, name, name)
3
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44 f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
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45 if not os.path.isdir(f):
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46 stop_err("Missing output folder")
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47 if not os.listdir(f):
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48 stop_err("Empty output folder")
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49 missing = []
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50 for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta),
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51 ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual),
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52 ("%s/%s_out.wig" % (f, name), out_wig),
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53 ("%s/%s_out.caf" % (f, name), out_caf),
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54 ("%s/%s_out.ace" % (f, name), out_ace)]:
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55 if not os.path.isfile(old):
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56 missing.append(os.path.splitext(old)[-1])
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57 else:
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58 shutil.move(old, new)
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59 if missing:
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60 stop_err("Missing output files: %s" % ", ".join(missing))
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61
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62 def clean_up(temp, name):
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63 folder = "%s/%s_assembly" % (temp, name)
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64 if os.path.isdir(folder):
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65 shutil.rmtree(folder)
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66
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67 #TODO - Run MIRA in /tmp or a configurable directory?
3
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68 #Currently Galaxy puts us somewhere safe like:
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69 #/opt/galaxy-dist/database/job_working_directory/846/
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70 temp = "."
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71 name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8]
3
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72
0
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73 start_time = time.time()
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74 cmd_list =sys.argv[8:]
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75 cmd = " ".join(cmd_list)
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76
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77 assert os.path.isdir(temp)
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78 d = "%s_assembly" % name
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79 assert not os.path.isdir(d), "Path %s already exists" % d
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80 try:
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81 #Check path access
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82 os.mkdir(d)
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83 except Exception, err:
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84 sys.stderr.write("Error making directory %s\n%s" % (d, err))
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85 sys.exit(1)
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86
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87 #print os.path.abspath(".")
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88 #print cmd
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89
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90 handle = open(out_log, "w")
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91 try:
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92 #Run MIRA
4
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93 child = subprocess.Popen(cmd_list,
3
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94 stdout=handle,
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95 stderr=subprocess.STDOUT)
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96 except Exception, err:
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97 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
3
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98 #TODO - call clean up?
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99 handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
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100 handle.close()
0
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101 sys.exit(1)
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102 #Use .communicate as can get deadlocks with .wait(),
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103 stdout, stderr = child.communicate()
3
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104 assert not stdout and not stderr #Should be empty as sent to handle
0
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105 run_time = time.time() - start_time
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106 return_code = child.returncode
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107 handle.write("\n\nMIRA took %0.2f minutes\n" % (run_time / 60.0))
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108 print "MIRA took %0.2f minutes" % (run_time / 60.0)
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109 if return_code:
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110 handle.write("Return error code %i from command:\n" % return_code)
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111 handle.write(cmd + "\n")
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112 handle.close()
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113 clean_up(temp, name)
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114 stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
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115 return_code)
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116 handle.close()
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117
4
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118 #print "Collecting output..."
0
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119 collect_output(temp, name)
4
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120
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121 #print "Cleaning up..."
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122 clean_up(temp, name)
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123
0
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124 print "Done"