Mercurial > repos > sanbi-uwc > build_ctb_gene

annotate build_ctb_gene.py @ 10:cb322069c7bc draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit f3af88f047a6081a46925bdbb50161ad1244b4f1
author sanbi-uwc
date Mon, 16 May 2016 10:34:46 -0400
parents 9cc174f0fb9f
children 517691812452
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1 #!/usr/bin/env python
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2 from __future__ import print_function
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3 import argparse
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4 import os
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5 import sys
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6 import glob
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7 import shlex
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8 import shutil
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9 from subprocess import check_call, CalledProcessError
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11 import logging
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13 log = logging.getLogger(__name__)
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16 class BuildCtbRunner(object):
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18 def __init__(self, args=None):
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19 '''
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20 Initializes an object to run CtbRunner in Galaxy.
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21 '''
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23 # Check whether the options are specified and saves them into the object
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24 assert args != None
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25 self.args = args
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27 def build_ctb_gene(self, output_file1, output_dir, input_file, mount_point):
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28 # cmdline_str = "build_ctb_gene goterms ${}".format(input_file)
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29 cmdline_str = "touch /tmp/foo.bar"
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30 build_ctb = False
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31 cmdline_str = self.newSplit(cmdline_str)
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32 try:
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33 check_call(cmdline_str)
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34 build_ctb = True
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35 except CalledProcessError:
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36 print("Error running the build_ctb_gene gotermS", file=sys.stderr)
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37
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38 # Read the files at the mount point and load the html file
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39 if build_ctb:
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40 files = glob.glob(mount_point)
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41 output_file1 = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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42 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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43 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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44 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
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45 <title></title>
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46 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
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47 </head>
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48 <body>
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49 <div class="toolFormBody">
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50 <table>
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51 <th>Files</th>
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52 """
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53 for f in files:
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54 output_file1 += "<tr><td>" + f + "</td></tr>"
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55 output_file1 += """</table></div></body></html>\n"""
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56
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57 self.copy_output_file_to_dataset()
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58 return output_file1
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59
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60 def newSplit(value):
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61 lex = shlex.shlex(value)
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62 lex.quotes = '"'
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63 lex.whitespace_split = True
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64 lex.commenters = ''
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65 return list(lex)
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66
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67 def copy_output_file_to_dataset(self):
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68 '''
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69 Retrieves the output files from the output directory and copies them to the Galaxy output files
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70 '''
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71
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72 # retrieve neo4j files to the working gx directory
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73 result_file = glob.glob(self.args.mount_point + '/*')
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74 with open(result_file[0], 'rb') as fsrc:
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75 with open(self.args.outputdir, 'wb') as fdest:
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76 shutil.copyfileobj(fsrc, fdest)
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79 def main():
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80 parser = argparse.ArgumentParser(description="Tool used to extract data about genes using locus_tags")
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81 parser.add_argument('output_file1')
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82 parser.add_argument('--outputdir')
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83 parser.add_argument('--input_file')
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84 parser.add_argument('--mount_point')
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85 parser.add_argument('--username')
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86 parser.add_argument('--password')
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87 parser.add_argument('--url')
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88 parser.add_argument('--port')
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89 args = parser.parse_args()
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90
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91 export_cmd = "export NEO4J_REST_URL=http://${args.username}:${args.password}@${args.url}:${args.port}/db/data/"
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92 try:
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93 os.system(export_cmd)
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94 except:
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95 log.debug("Error exporting the NEO4J db environmental values")
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96
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97 # make the output directory
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98 if not os.path.exists(args.outputdir):
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99 os.makedirs(args.outputdir)
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100
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101 ctb_gene_runner = BuildCtbRunner(args)
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102 ctb_gene_runner.build_ctb_gene(args.output_file1, args.outputdir, args.input_file, args.mount_point)
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103
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104
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105 if __name__ == "__main__": main()