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annotate bismark_methylation_extractor.py @ 14:b6aa3b6ba129 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
author bgruening
date Tue, 30 Jul 2019 10:33:02 -0400
parents 9bfe38410155
children ff6ee551b153
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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
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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13 from glob import glob
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14
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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))
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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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):
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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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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41
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42 def build_genome_dir(genome_file):
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43 tmp_genome_dir = tempfile.mkdtemp(prefix='tmp')
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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44 genome_path = os.path.join(tmp_genome_dir, '.'.join(os.path.split(genome_file)[1].split('.')[:-1]))
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45 try:
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46 # Create a hard link pointing to genome_file named 'genome_path'.fa.
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47 os.symlink(genome_file, genome_path + '.fa')
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48 except Exception as e:
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49 if os.path.exists(tmp_genome_dir):
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50 shutil.rmtree(tmp_genome_dir)
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51 stop_err('Error in linking the reference database!\n%s' % e)
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52 return tmp_genome_dir
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53
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54
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55 def __main__():
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56 # Parse Command Line
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57 parser = argparse.ArgumentParser(description='Wrapper for the bismark methylation caller.')
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58
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59 # input options
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60 parser.add_argument('--infile', help='Input file in SAM or BAM format.')
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61 parser.add_argument('--single-end', dest='single_end', action="store_true")
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62 parser.add_argument('--paired-end', dest='paired_end', action="store_true")
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63
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64 parser.add_argument('--multicore', dest='multicore', type=int, default=1)
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65 parser.add_argument('--splitting_report', dest='splitting_report')
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66 parser.add_argument('--mbias_report', dest='mbias_report')
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67 parser.add_argument('--cytosine_report', dest="cytosine_report")
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68 parser.add_argument('--genome_file', dest="genome_file")
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69 parser.add_argument('--cx_context', action="store_true")
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70
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71 parser.add_argument('--comprehensive', action="store_true")
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72 parser.add_argument('--merge-non-cpg', dest='merge_non_cpg', action="store_true")
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73 parser.add_argument('--no-overlap', dest='no_overlap', action="store_true")
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74 parser.add_argument('--compress', dest='compress')
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75 parser.add_argument('--ignore', dest='ignore', type=int)
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76 parser.add_argument('--ignore_r2', dest='ignore_r2', type=int)
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77 parser.add_argument('--ignore_3prime', dest='ignore_3prime', type=int)
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78 parser.add_argument('--ignore_3prime_r2', dest='ignore_3prime_r2', type=int)
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79 parser.add_argument('--log_report', dest='log_report', metavar='log_filename', type=str)
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80 args = parser.parse_args()
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81
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82 logger = logging.getLogger('bismark_methylation_extractor_wrapper')
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83 logger.setLevel(logging.DEBUG)
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84 ch = logging.StreamHandler(sys.stdout)
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85 if args.log_report:
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86 ch.setLevel(logging.WARNING)
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87 handler = logging.FileHandler(args.log_report)
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88 handler.setLevel(logging.DEBUG)
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89 logger.addHandler(handler)
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90 else:
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91 ch.setLevel(logging.DEBUG)
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92 logger.addHandler(ch)
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93
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94 # Build methylation extractor command
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95 output_dir = tempfile.mkdtemp()
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96 cmd = ['bismark_methylation_extractor', '--no_header', '-o', output_dir]
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97 # Set up all options
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98 if args.multicore > 3:
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99 # divide multicore by 3 here since bismark will spawn ~3 jobs.
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100 cmd.extend(['--multicore', str(math.ceil(args.multicore / 3))])
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101 if args.single_end:
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102 cmd.append('--single-end')
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103 else:
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104 cmd.append('--paired-end')
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105 if args.no_overlap:
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106 cmd.append('--no_overlap')
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107 if args.ignore:
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108 cmd.extend(['--ignore', str(args.ignore)])
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109 if args.ignore_r2:
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110 cmd.extend(['--ignore_r2', str(args.ignore_r2)])
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111 if args.ignore_3prime:
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112 cmd.extend(['--ignore_3prime', str(args.ignore_3prime)])
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113 if args.ignore_3prime_r2:
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114 cmd.extend(['--ignore_3prime_r2', str(args.ignore_3prime_r2)])
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115 if args.comprehensive:
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116 cmd.append('--comprehensive')
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117 if args.merge_non_cpg:
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118 cmd.append('--merge_non_CpG')
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119 if args.splitting_report:
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120 cmd.append('--report')
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121 tmp_genome_dir = None
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122 if args.cytosine_report:
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123 tmp_genome_dir = build_genome_dir(args.genome_file)
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124 if args.cx_context:
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125 cmd.extend(
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126 ['--bedGraph', '--CX_context', '--cytosine_report', '--CX_context', '--genome_folder', tmp_genome_dir])
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127 else:
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128 cmd.extend(['--bedGraph', '--cytosine_report', '--genome_folder', tmp_genome_dir])
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129
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130 cmd.append(args.infile)
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131
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132 # Run
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133 logger.info("Methylation extractor run with: '%s'", " ".join(cmd))
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134 prev_dir = os.getcwd()
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135 os.chdir(output_dir) # needed due to a bug in bismark where the coverage file cannot be found
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136 process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
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137 with process.stdout:
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138 log_subprocess_output(logger, process.stdout)
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139 exitcode = process.wait()
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140 if exitcode != 0:
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141 stop_err(logger, "Bismark methylation extractor error (also check the log file if any)!\n%s" % process.stderr)
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142 logger.info("Finished methylation extractor.")
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143 # collect and copy output files
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144 logger.debug("Zip output files to '%s'.", args.compress)
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145 os.chdir(prev_dir)
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146 zipper(output_dir, args.compress)
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147
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148 # cytosine report
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149 if args.cytosine_report:
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150 logger.debug("Collecting cytosine report.")
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151 if args.cx_context:
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152 shutil.move(glob(os.path.join(output_dir, '*CX_report.txt'))[0], args.cytosine_report)
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153 else:
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154 shutil.move(glob(os.path.join(output_dir, '*CpG_report.txt'))[0], args.cytosine_report)
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155 # splitting report
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156 if args.splitting_report:
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157 logger.debug("Collecting splitting report.")
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158 shutil.move(glob(os.path.join(output_dir, '*_splitting_report.txt'))[0], args.splitting_report)
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159 if args.mbias_report:
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160 logger.debug("Collecting M-Bias file.")
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161 shutil.move(glob(os.path.join(output_dir, '*M-bias.txt'))[0], args.mbias_report)
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162
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163 # Clean up temp dirs
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164 logger.debug("Cleanup temp dirs.")
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165 if os.path.exists(output_dir):
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166 shutil.rmtree(output_dir)
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167 if tmp_genome_dir and os.path.exists(tmp_genome_dir):
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168 shutil.rmtree(tmp_genome_dir)
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169 logger.info("Done.")
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170
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171 if __name__ == "__main__": __main__()