Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4_0/mira4_bait.py @ 39:bbf14bb9607b draft default tip

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
author peterjc
date Mon, 03 Jun 2019 13:29:00 -0400
parents cee8f9005e43
children
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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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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 = "0.0.11" # Keep in sync with the XML file
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15 def get_version(mira_binary):
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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_binary, "-v"]
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20 try:
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21 child = subprocess.Popen(
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22 cmd,
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23 universal_newlines=True,
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24 stdout=subprocess.PIPE,
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25 stderr=subprocess.STDOUT,
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26 )
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27 except Exception as err:
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28 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
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29 sys.exit(1)
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30 ver, tmp = child.communicate()
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31 del child
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32 # Workaround for -v not working in mirabait 4.0RC4
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33 if "invalid option" in ver.split("\n", 1)[0]:
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34 for line in ver.split("\n", 1):
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35 if " version " in line:
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36 line = line.split()
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37 return line[line.index("version") + 1].rstrip(")")
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38 sys.exit("Could not determine MIRA version:\n%s" % ver)
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39 return ver.split("\n", 1)[0]
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40
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42 if "MIRA4" in os.environ:
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43 mira_path = os.environ["MIRA4"]
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44 mira_binary = os.path.join(mira_path, "mirabait")
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45 if not os.path.isfile(mira_binary):
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46 sys.exit(
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47 "Missing mirabait under $MIRA4, %r\nFolder contained: %s"
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48 % (mira_binary, ", ".join(os.listdir(mira_path)))
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49 )
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50 else:
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51 sys.stderr.write(
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52 "DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n"
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53 )
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54 mira_path = None
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55 mira_binary = "mirabait"
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56
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57 mira_ver = get_version(mira_binary)
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58 if not mira_ver.strip().startswith("4.0"):
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59 sys.exit("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver)
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60 if "-v" in sys.argv or "--version" in sys.argv:
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61 print("%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER))
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62 sys.exit(0)
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64
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65 (
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66 format,
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67 output_choice,
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68 strand_choice,
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69 kmer_length,
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70 min_occurance,
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71 bait_file,
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72 in_file,
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73 out_file,
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74 ) = sys.argv[1:]
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75
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76 if format.startswith("fastq"):
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77 format = "fastq"
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78 elif format == "mira":
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79 format = "maf"
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80 elif format != "fasta":
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81 sys.exit("Was not expected format %r" % format)
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82
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83 assert out_file.endswith(".dat")
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84 out_file_stem = out_file[:-4]
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85
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86 cmd_list = [
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87 mira_binary,
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88 "-f",
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89 format,
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90 "-t",
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91 format,
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92 "-k",
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93 kmer_length,
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94 "-n",
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95 min_occurance,
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96 bait_file,
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97 in_file,
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98 out_file_stem,
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99 ]
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100 if output_choice == "pos":
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101 pass
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102 elif output_choice == "neg":
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103 # Invert the selection...
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104 cmd_list.insert(1, "-i")
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105 else:
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106 sys.exit("Output choice should be 'pos' or 'neg', not %r" % output_choice)
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107 if strand_choice == "both":
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108 pass
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109 elif strand_choice == "fwd":
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110 # Ingore reverse strand...
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111 cmd_list.insert(1, "-r")
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112 else:
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113 sys.exit("Strand choice should be 'both' or 'fwd', not %r" % strand_choice)
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114
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115 cmd = " ".join(cmd_list)
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116 # print cmd
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117 start_time = time.time()
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118 try:
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119 # Run MIRA
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120 child = subprocess.Popen(
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121 cmd_list,
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122 universal_newlines=True,
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123 stdout=subprocess.PIPE,
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124 stderr=subprocess.STDOUT,
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125 )
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126 except Exception as err:
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127 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
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128 sys.exit(1)
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129 # Use .communicate as can get deadlocks with .wait(),
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130 stdout, stderr = child.communicate()
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131 assert stderr is None # Due to way we ran with subprocess
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132 run_time = time.time() - start_time
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133 return_code = child.returncode
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134 print("mirabait took %0.2f minutes" % (run_time / 60.0))
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135
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136 if return_code:
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137 sys.stderr.write(stdout)
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138 sys.exit("Return error code %i from command:\n%s" % (return_code, cmd), return_code)
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139
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140 # Capture output
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141 out_tmp = out_file_stem + "." + format
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142 if not os.path.isfile(out_tmp):
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143 sys.stderr.write(stdout)
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144 sys.exit("Missing output file from mirabait: %s" % out_tmp)
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145 shutil.move(out_tmp, out_file)