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annotate bismark_pretty_report/bismark2report_wrapper.py @ 7:fcadce4d9a06 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
author bgruening
date Sat, 06 May 2017 13:18:09 -0400
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7
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1 #!/usr/bin/python
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2
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3 import argparse
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4 import os
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5 import shutil
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6 import subprocess
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7 import sys
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8 import tempfile
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9 import logging
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10
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11 def cleanup_before_exit(tmp_dir):
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12 if tmp_dir and os.path.exists(tmp_dir):
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13 shutil.rmtree(tmp_dir)
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14
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15 def get_arg():
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16 parser = argparse.ArgumentParser()
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17 parser.add_argument('--tool_dir', dest='tool_dir', action='store', nargs=1, metavar='tool_dir', type=str)
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18 parser.add_argument('--alignment_report', dest='alignment_report', action='store', nargs=1, metavar='alignment_report', type=str)
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19 parser.add_argument('--dedup_report', dest='dedup_report', action='store', nargs=1, metavar='dedup_report', type=str)
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20 parser.add_argument('--splitting_report', dest='splitting_report', action='store', nargs=1, metavar='splitting_report', type=str)
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21 parser.add_argument('--mbias_report', dest='mbias_report', action='store', nargs=1, metavar='mbias_report', type=str)
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22 parser.add_argument('--nucleotide_report', dest='nucleotide_report', action='store', nargs=1, metavar='nucleotide_report', type=str)
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23 parser.add_argument('--output_html_report', dest='output_html_report', action='store', nargs=1, metavar='output_html_report', type=str)
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24 parser.add_argument('--output_html_report_link', dest='output_html_report_link', action='store', nargs=1, metavar='output_html_report_link', type=str)
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25 parser.add_argument('--log_report', dest='log_report', action='store', nargs=1, metavar='log_report', type=str)
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26 parser.add_argument('--output_dir', dest='job_dir', action='store', nargs=1, metavar='job_dir', type=str)
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27 args = parser.parse_args()
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28 return args
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29
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30 def create_and_write_html_link(job_dir, output_html_report_link, tmp_dir):
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31 """
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32 Web browsers don't allow to open a link pointing to the absolute path of a local html file FROM a website page;
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33 The only way to make such link functional is to integrate the local file inside the web structure of the site.
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34 Galaxy has been designed such that the child_dir <dataset_[0-9]+_files> of the output_dir is considered as the root
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35 of the html base tag (i.e <base href="/" /> for the current job running.
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36 The function proceeds the following steps:
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37 #1. Extracts the galaxy dir where the output files are stored
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38 #2. Creating a child dir <dataset_[0-9]+_files> in this output_dir is needed because it is considered as the root of the html base tag
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39 # We can extract the exact name of this child dir from the jobs_directory name
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40 #3. Moves the html file in this child_dir
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41 """
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42 output_path_list = output_html_report_link.split('/')
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43 output_path = '/'.join(output_path_list[0:-1])
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44 html_root = job_dir.split('/')[-1]
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45 final_dir = os.path.join(output_path, html_root)
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46 os.makedirs(final_dir)
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47 shutil.move(os.path.join(tmp_dir, 'html_report'), os.path.join(final_dir, 'html_report.html'))
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48
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49 html_report = open(output_html_report_link, 'wb')
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50 html_report.write('<!DOCTYPE html>\n')
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51 html_report.write('<head>\n')
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52 html_report.write('\t<meta http-equiv="content-type" content="text/html; charset=UTF-8">\n')
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53 html_report.write('\t\t<base href="/" />\n')
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54 html_report.write('\t\t<a href="html_report.html/" target="_blank">Link to Bismark Pretty Report Page</a>\n')
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55 html_report.write('</head>')
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56 html_report.close()
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57
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58 def __main__():
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59 args = get_arg()
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60
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61 tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='')
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62
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63 if args.log_report:
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64 logging.basicConfig(level=logging.INFO, filename=args.log_report[0], filemode="a+", format='%(message)s')
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65 else:
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66 logging.basicConfig(level=logging.INFO, filename=os.path.join(tmp_dir, 'log_report.txt'), filemode="a+", format='%(message)s')
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67
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68 alignment_option = '--alignment_report'
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69 alignment_report = args.alignment_report[0]
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70 if args.dedup_report:
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71 dedup_option = '--dedup_report'
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72 dedup_report = args.dedup_report[0]
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73 else:
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74 dedup_option = ''
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75 dedup_report = ''
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76 if args.splitting_report:
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77 splitting_option = '--splitting_report'
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78 splitting_report = args.splitting_report[0]
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79 else:
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80 splitting_option = ''
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81 splitting_report = ''
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82 if args.mbias_report:
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83 mbias_option = '--mbias_report'
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84 mbias_report = args.mbias_report[0]
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85 else:
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86 mbias_option = ''
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87 mbias_report = ''
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88 if args.nucleotide_report:
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89 nucleotide_option = '--nucleotide_report'
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90 nucleotide_report = args.nucleotide_report[0]
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91 else:
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92 nucleotide_option = ''
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93 nucleotide_report = ''
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94
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95 proc = subprocess.Popen(['perl', os.path.join(args.tool_dir[0], 'bismark2report'), alignment_option, alignment_report, dedup_option, dedup_report,\
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96 splitting_option, splitting_report, mbias_option, mbias_report, nucleotide_option, nucleotide_report,\
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97 '--dir', tmp_dir, '--output', 'html_report'],\
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98 stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
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99 proc_out, proc_err = proc.communicate()
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100
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101 cmd = 'perl %s %s %s %s %s %s %s %s %s %s %s --output html_report --dir %s'\
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102 % (os.path.join(args.tool_dir[0], 'bismark2report'), alignment_option, alignment_report, dedup_option, dedup_report,\
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103 splitting_option, splitting_report, mbias_option, mbias_report, nucleotide_option, nucleotide_report, tmp_dir)
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104
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105 logging.info('COMMAND LINE:\n\n%s' % cmd)
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106 logging.info("__________________________________________________________________\n")
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107 logging.info("BISMARK PRETTY REPORT STDOUT:\n\n%s" % proc_out)
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108 if proc_err:
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109 logging.critical("__________________________________________________________________\n")
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110 logging.critical("BISMARK PRETTY REPORT ERROR:\n\n%s" % proc_err)
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111 sys.exit("Bismark pretty report crashed with the folowing error message:\n%s" % proc_err)
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112
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113 if args.output_html_report:
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114 shutil.copy(os.path.join(tmp_dir, 'html_report'), args.output_html_report[0])
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115
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116 #This function writes a link towards the Bismark html page inside an html file.
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117 #This is needed because the direct visualization of the Bismark html report via Galaxy is ugly
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118 create_and_write_html_link(args.job_dir[0], args.output_html_report_link[0], tmp_dir)
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119
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120 cleanup_before_exit(tmp_dir)
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121
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122 if __name__=="__main__": __main__()