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annotate bismark_methylation_extractor.py @ 38:b2d0e92f81c2 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
author bgruening
date Thu, 22 Apr 2021 17:05:07 +0000
parents 79df147da633
children
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1 #!/usr/bin/env python
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3 import argparse
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4 import logging
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5 import math
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6 import os
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7 import re
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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 tempfile
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12 import zipfile
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13 from glob import glob
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16 def stop_err(logger, msg):
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17 logger.critical(msg)
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18 sys.exit(1)
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21 def log_subprocess_output(logger, pipe):
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22 for line in iter(pipe.readline, b""):
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23 logger.debug(line.decode().rstrip())
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26 def zipper(dir, zip_file):
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27 output_files_regex = re.compile("^(Non_)?C[pH][GH]_.*")
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28 bedgraph_regex = re.compile(".*bedGraph.gz")
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29 zip = zipfile.ZipFile(zip_file, "w", compression=zipfile.ZIP_DEFLATED)
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30 root_len = len(os.path.abspath(dir))
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31 for root, dirs, files in os.walk(dir):
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32 archive_root = os.path.abspath(root)[root_len:]
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33 for f in files:
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34 if re.search(output_files_regex, f) or re.search(bedgraph_regex, f):
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35 fullpath = os.path.join(root, f)
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36 archive_name = os.path.join(archive_root, f)
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37 zip.write(fullpath, archive_name, zipfile.ZIP_DEFLATED)
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38 zip.close()
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39 return zip_file
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42 def build_genome_dir(genome_file):
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43 tmp_genome_dir = tempfile.mkdtemp(prefix="tmp")
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44 genome_path = os.path.join(
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45 tmp_genome_dir, ".".join(os.path.split(genome_file)[1].split(".")[:-1])
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46 )
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47 try:
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48 # Create a hard link pointing to genome_file named 'genome_path'.fa.
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49 os.symlink(genome_file, genome_path + ".fa")
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50 except Exception as e:
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51 if os.path.exists(tmp_genome_dir):
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52 shutil.rmtree(tmp_genome_dir)
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53 stop_err("Error in linking the reference database!\n%s" % e)
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54 return tmp_genome_dir
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57 def __main__():
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58 # Parse Command Line
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59 parser = argparse.ArgumentParser(
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60 description="Wrapper for the bismark methylation caller."
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61 )
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63 # input options
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64 parser.add_argument("--infile", help="Input file in SAM or BAM format.")
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65 parser.add_argument("--single-end", dest="single_end", action="store_true")
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66 parser.add_argument("--paired-end", dest="paired_end", action="store_true")
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68 parser.add_argument("--multicore", dest="multicore", type=int, default=1)
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69 parser.add_argument("--splitting_report", dest="splitting_report")
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70 parser.add_argument("--mbias_report", dest="mbias_report")
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71 parser.add_argument("--cytosine_report", dest="cytosine_report")
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72 parser.add_argument("--genome_file", dest="genome_file")
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73 parser.add_argument("--cx_context", action="store_true")
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74
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75 parser.add_argument("--comprehensive", action="store_true")
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76 parser.add_argument("--merge-non-cpg", dest="merge_non_cpg", action="store_true")
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77 parser.add_argument("--no-overlap", dest="no_overlap", action="store_true")
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78 parser.add_argument("--compress", dest="compress")
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79 parser.add_argument("--ignore", dest="ignore", type=int)
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80 parser.add_argument("--ignore_r2", dest="ignore_r2", type=int)
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81 parser.add_argument("--ignore_3prime", dest="ignore_3prime", type=int)
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82 parser.add_argument("--ignore_3prime_r2", dest="ignore_3prime_r2", type=int)
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83 parser.add_argument(
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84 "--log_report", dest="log_report", metavar="log_filename", type=str
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85 )
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86 args = parser.parse_args()
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87
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88 logger = logging.getLogger("bismark_methylation_extractor_wrapper")
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89 logger.setLevel(logging.DEBUG)
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90 ch = logging.StreamHandler(sys.stdout)
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91 if args.log_report:
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92 ch.setLevel(logging.WARNING)
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93 handler = logging.FileHandler(args.log_report)
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94 handler.setLevel(logging.DEBUG)
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95 logger.addHandler(handler)
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96 else:
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97 ch.setLevel(logging.DEBUG)
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98 logger.addHandler(ch)
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99
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100 # Build methylation extractor command
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101 output_dir = tempfile.mkdtemp()
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102 cmd = ["bismark_methylation_extractor", "--no_header", "-o", output_dir]
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103 # Set up all options
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104 if args.multicore > 3:
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105 # divide multicore by 3 here since bismark will spawn ~3 jobs.
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106 cmd.extend(["--multicore", str(int(math.floor(args.multicore / 3)))])
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107 if args.single_end:
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108 cmd.append("--single-end")
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109 else:
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110 cmd.append("--paired-end")
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111 if args.no_overlap:
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112 cmd.append("--no_overlap")
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113 if args.ignore:
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114 cmd.extend(["--ignore", str(args.ignore)])
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115 if args.ignore_r2:
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116 cmd.extend(["--ignore_r2", str(args.ignore_r2)])
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117 if args.ignore_3prime:
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118 cmd.extend(["--ignore_3prime", str(args.ignore_3prime)])
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119 if args.ignore_3prime_r2:
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120 cmd.extend(["--ignore_3prime_r2", str(args.ignore_3prime_r2)])
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121 if args.comprehensive:
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122 cmd.append("--comprehensive")
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123 if args.merge_non_cpg:
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124 cmd.append("--merge_non_CpG")
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125 if args.splitting_report:
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126 cmd.append("--report")
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127 tmp_genome_dir = None
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128 if args.cytosine_report:
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129 tmp_genome_dir = build_genome_dir(args.genome_file)
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130 if args.cx_context:
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131 cmd.extend(
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132 [
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133 "--bedGraph",
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134 "--CX_context",
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135 "--cytosine_report",
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136 "--CX_context",
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137 "--genome_folder",
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138 tmp_genome_dir,
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139 ]
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140 )
25
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141 else:
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142 cmd.extend(
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143 ["--bedGraph", "--cytosine_report", "--genome_folder", tmp_genome_dir]
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144 )
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145
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146 cmd.append(args.infile)
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147
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148 # Run
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149 logger.info("Methylation extractor run with: '%s'", " ".join(cmd))
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150 prev_dir = os.getcwd()
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151 os.chdir(
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152 output_dir
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153 ) # needed due to a bug in bismark where the coverage file cannot be found
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154 process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
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155 with process.stdout:
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156 log_subprocess_output(logger, process.stdout)
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157 exitcode = process.wait()
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158 if exitcode != 0:
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159 stop_err(
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160 logger,
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161 "Bismark methylation extractor error (also check the log file if any)!\n%s"
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162 % process.stderr,
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163 )
25
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164 logger.info("Finished methylation extractor.")
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165 # collect and copy output files
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166 logger.debug("Zip output files to '%s'.", args.compress)
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167 os.chdir(prev_dir)
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168 zipper(output_dir, args.compress)
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169
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170 # cytosine report
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171 if args.cytosine_report:
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172 logger.debug("Collecting cytosine report.")
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173 if args.cx_context:
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174 shutil.move(
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175 glob(os.path.join(output_dir, "*CX_report.txt"))[0],
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176 args.cytosine_report,
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177 )
25
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178 else:
38
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179 shutil.move(
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180 glob(os.path.join(output_dir, "*CpG_report.txt"))[0],
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181 args.cytosine_report,
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182 )
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183 # splitting report
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184 if args.splitting_report:
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185 logger.debug("Collecting splitting report.")
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186 shutil.move(
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187 glob(os.path.join(output_dir, "*_splitting_report.txt"))[0],
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188 args.splitting_report,
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189 )
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190 if args.mbias_report:
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191 logger.debug("Collecting M-Bias file.")
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192 shutil.move(glob(os.path.join(output_dir, "*M-bias.txt"))[0], args.mbias_report)
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193
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194 # Clean up temp dirs
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195 logger.debug("Cleanup temp dirs.")
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196 if os.path.exists(output_dir):
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197 shutil.rmtree(output_dir)
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198 if tmp_genome_dir and os.path.exists(tmp_genome_dir):
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199 shutil.rmtree(tmp_genome_dir)
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200 logger.info("Done.")
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201
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202
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203 if __name__ == "__main__":
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204 __main__()