Mercurial > repos > peterjc > mira_assembler

annotate tools/mira3/mira.py @ 27:85b86f31327c draft

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira3/ commit 206259620376b322fc8ed99a6efdd3712f38764b
author peterjc
date Wed, 11 Jul 2018 12:34:58 -0400
parents ad14a345f1b0
children e28d6015fc56
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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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4 from __future__ import print_function
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5
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6 import os
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7 import shutil
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8 import subprocess
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9 import sys
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10 import time
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11
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12 WRAPPER_VER = "0.0.12" # Keep in sync with the XML file
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15 def get_version():
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16 """Run MIRA to find its version number."""
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17 # At the commend line I would use: mira -v | head -n 1
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18 # however there is some pipe error when doing that here.
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19 cmd = ["mira", "-v"]
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20 try:
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21 child = subprocess.Popen(cmd, universal_newlines=True,
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22 stdout=subprocess.PIPE,
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23 stderr=subprocess.STDOUT)
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24 except Exception as err:
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25 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
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26 sys.exit(1)
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27 ver, tmp = child.communicate()
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28 del child
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29 return ver.split("\n", 1)[0]
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32 mira_ver = get_version()
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33 if "V3.4." not in mira_ver:
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34 sys.exit("This wrapper is for MIRA V3.4, not %s" % mira_ver)
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35 if "-v" in sys.argv:
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36 print("MIRA wrapper version %s," % WRAPPER_VER)
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37 print(mira_ver)
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38 sys.exit(0)
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41 def collect_output(temp, name):
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42 f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
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43 if not os.path.isdir(f):
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44 sys.exit("Missing output folder")
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45 if not os.listdir(f):
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46 sys.exit("Empty output folder")
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47 missing = []
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48 for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta),
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49 ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual),
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50 ("%s/%s_out.wig" % (f, name), out_wig),
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51 ("%s/%s_out.caf" % (f, name), out_caf),
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52 ("%s/%s_out.ace" % (f, name), out_ace)]:
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53 if not os.path.isfile(old):
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54 missing.append(os.path.splitext(old)[-1])
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55 else:
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56 shutil.move(old, new)
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57 if missing:
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58 sys.exit("Missing output files: %s" % ", ".join(missing))
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60
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61 def clean_up(temp, name):
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62 folder = "%s/%s_assembly" % (temp, name)
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63 if os.path.isdir(folder):
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64 shutil.rmtree(folder)
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65
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67 # TODO - Run MIRA in /tmp or a configurable directory?
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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]
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72
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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 as 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
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93 child = subprocess.Popen(cmd_list, universal_newlines=True,
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94 stdout=handle,
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95 stderr=subprocess.STDOUT)
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96 except Exception as err:
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97 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
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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()
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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()
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104 assert not stdout and not stderr # Should be empty as sent to handle
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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 sys.stderr.write("Return error code %i from command:\n" % return_code)
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115 sys.stderr.write(cmd + "\n")
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116 sys.exit(return_code)
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117 handle.close()
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118
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119 # print "Collecting output..."
12
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120 collect_output(temp, name)
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121
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122 # print "Cleaning up..."
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123 clean_up(temp, name)
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124
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125 print("Done")