Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4_0/mira4_bait.py @ 35:259891fce7fd draft

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
author peterjc
date Wed, 09 Aug 2017 13:32:11 -0400
parents 0785a6537f3e
children cee8f9005e43
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1 #!/usr/bin/env python
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2 """A simple wrapper script to call MIRA4's mirabait and collect its output.
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3 """
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5 from __future__ import print_function
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6
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7 import os
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8 import shutil
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9 import subprocess
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10 import sys
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11 import time
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12
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13 WRAPPER_VER = "0.0.11" # Keep in sync with the XML file
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16 def get_version(mira_binary):
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17 """Run MIRA to find its version number"""
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18 # At the commend line I would use: mira -v | head -n 1
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19 # however there is some pipe error when doing that here.
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20 cmd = [mira_binary, "-v"]
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21 try:
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22 child = subprocess.Popen(cmd, universal_newlines=True,
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23 stdout=subprocess.PIPE,
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24 stderr=subprocess.STDOUT)
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25 except Exception as 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 # Workaround for -v not working in mirabait 4.0RC4
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31 if "invalid option" in ver.split("\n", 1)[0]:
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32 for line in ver.split("\n", 1):
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33 if " version " in line:
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34 line = line.split()
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35 return line[line.index("version") + 1].rstrip(")")
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36 sys.exit("Could not determine MIRA version:\n%s" % ver)
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37 return ver.split("\n", 1)[0]
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38
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40 if "MIRA4" in os.environ:
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41 mira_path = os.environ["MIRA4"]
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42 mira_binary = os.path.join(mira_path, "mirabait")
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43 if not os.path.isfile(mira_binary):
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44 sys.exit("Missing mirabait under $MIRA4, %r\nFolder contained: %s"
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45 % (mira_binary, ", ".join(os.listdir(mira_path))))
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46 else:
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47 sys.stderr.write("DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n")
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48 mira_path = None
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49 mira_binary = "mirabait"
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50
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51 mira_ver = get_version(mira_binary)
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52 if not mira_ver.strip().startswith("4.0"):
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53 sys.exit("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver)
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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 sys.exit(0)
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59 format, output_choice, strand_choice, kmer_length, min_occurance, bait_file, in_file, out_file = sys.argv[1:]
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60
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61 if format.startswith("fastq"):
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62 format = "fastq"
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63 elif format == "mira":
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64 format = "maf"
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65 elif format != "fasta":
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66 sys.exit("Was not expected format %r" % format)
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67
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68 assert out_file.endswith(".dat")
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69 out_file_stem = out_file[:-4]
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70
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71 cmd_list = [mira_binary, "-f", format, "-t", format,
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72 "-k", kmer_length, "-n", min_occurance,
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73 bait_file, in_file, out_file_stem]
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74 if output_choice == "pos":
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75 pass
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76 elif output_choice == "neg":
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77 # Invert the selection...
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78 cmd_list.insert(1, "-i")
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79 else:
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80 sys.exit("Output choice should be 'pos' or 'neg', not %r" % output_choice)
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81 if strand_choice == "both":
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82 pass
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83 elif strand_choice == "fwd":
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84 # Ingore reverse strand...
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85 cmd_list.insert(1, "-r")
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86 else:
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87 sys.exit("Strand choice should be 'both' or 'fwd', not %r" % strand_choice)
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88
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89 cmd = " ".join(cmd_list)
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90 # print cmd
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91 start_time = time.time()
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92 try:
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93 # Run MIRA
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94 child = subprocess.Popen(cmd_list, universal_newlines=True,
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95 stdout=subprocess.PIPE,
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96 stderr=subprocess.STDOUT)
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97 except Exception as err:
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98 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
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99 sys.exit(1)
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100 # Use .communicate as can get deadlocks with .wait(),
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101 stdout, stderr = child.communicate()
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102 assert stderr is None # Due to way we ran with subprocess
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103 run_time = time.time() - start_time
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104 return_code = child.returncode
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105 print("mirabait took %0.2f minutes" % (run_time / 60.0))
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106
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107 if return_code:
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108 sys.stderr.write(stdout)
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109 sys.exit("Return error code %i from command:\n%s" % (return_code, cmd),
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110 return_code)
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111
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112 # Capture output
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113 out_tmp = out_file_stem + "." + format
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114 if not os.path.isfile(out_tmp):
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115 sys.stderr.write(stdout)
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116 sys.exit("Missing output file from mirabait: %s" % out_tmp)
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117 shutil.move(out_tmp, out_file)