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annotate bismark2report_wrapper.py @ 22:8c191acde702 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 3005cec91ca52f9d28aa2fe0bd4190555abafc35
author bgruening
date Tue, 01 Aug 2023 11:42:10 +0000
parents 120b7b35e442
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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1 #!/usr/bin/python
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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3 import argparse
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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4 import logging
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5 import subprocess
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6 import sys
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9 def stop_err(logger, msg):
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10 logger.critical(msg)
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11 sys.exit()
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9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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14 def log_subprocess_output(logger, pipe):
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15 for line in iter(pipe.readline, b""):
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9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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16 logger.debug(line.decode().rstrip())
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19 def get_arg():
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20 parser = argparse.ArgumentParser()
21
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21 parser.add_argument(
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22 "--alignment_report",
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23 dest="alignment_report",
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24 action="store",
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25 metavar="alignment_report",
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26 type=str,
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27 )
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28 parser.add_argument(
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29 "--dedup_report",
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30 dest="dedup_report",
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31 action="store",
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32 metavar="dedup_report",
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33 type=str,
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34 )
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35 parser.add_argument(
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36 "--splitting_report",
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37 dest="splitting_report",
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38 action="store",
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39 metavar="splitting_report",
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40 type=str,
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41 )
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42 parser.add_argument(
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43 "--mbias_report",
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44 dest="mbias_report",
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45 action="store",
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46 metavar="mbias_report",
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47 type=str,
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48 )
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49 parser.add_argument(
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50 "--nucleotide_report",
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51 dest="nucleotide_report",
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52 action="store",
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53 metavar="nucleotide_report",
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54 type=str,
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55 )
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56 parser.add_argument(
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57 "--output_html_report",
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58 dest="output_html_report",
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59 action="store",
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60 metavar="output_html_report",
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61 type=str,
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62 )
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63 parser.add_argument(
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64 "--log_report",
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65 dest="log_report",
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66 action="store",
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67 metavar="log_report",
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68 type=str,
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69 )
8
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70 args = parser.parse_args()
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71 return args
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72
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73
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74 def __main__():
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75 args = get_arg()
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76 logger = logging.getLogger("bismark_deduplicate_wrapper")
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77 logger.setLevel(logging.DEBUG)
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78 ch = logging.StreamHandler(sys.stdout)
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79 if args.log_report:
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80 ch.setLevel(logging.WARNING)
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81 handler = logging.FileHandler(args.log_report)
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82 handler.setLevel(logging.DEBUG)
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83 logger.addHandler(handler)
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84 else:
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85 ch.setLevel(logging.DEBUG)
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86 logger.addHandler(ch)
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87
21
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88 cmd = [
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89 "bismark2report",
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90 "--verbose",
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91 "--alignment_report",
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92 args.alignment_report,
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93 "--output",
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94 args.output_html_report,
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95 ]
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96
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97 if args.dedup_report:
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98 cmd.extend(["--dedup_report", args.dedup_report])
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99 if args.splitting_report:
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100 cmd.extend(["--splitting_report", args.splitting_report])
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101 if args.mbias_report:
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102 cmd.extend(["--mbias_report", args.mbias_report])
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103 if args.nucleotide_report:
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104 cmd.extend(["--nucleotide_report", args.nucleotide_report])
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105
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106 logger.info("Generating report with: '%s'", " ".join(cmd))
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107 process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
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108 with process.stdout:
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109 log_subprocess_output(logger, process.stdout)
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110 exitcode = process.wait()
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111 if exitcode != 0:
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112 stop_err(
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113 logger,
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114 "Bismark pretty report error (also check the log file if any)!\n%s"
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115 % process.stderr,
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116 )
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117
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118
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119 if __name__ == "__main__":
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120 __main__()