Mercurial > repos > sanbi-uwc > build_ctb_gene

annotate build_ctb_gene.py @ 26:51a48982f643 draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit a8d49944fccca430c0d79782f01e8e8758161cb8
author sanbi-uwc
date Fri, 20 May 2016 06:25:15 -0400
parents 329bd8a876a6
children 3995dfb6b497
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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 import datetime
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10 from subprocess import check_call, CalledProcessError
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12 import logging
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14 log = logging.getLogger(__name__)
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17 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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22 # Check whether the options are specified and saves them into the object
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23 # assert args != None
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24 self.args = args
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26 def build_ctb_gene(self):
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27 cmdline_str = "build_ctb_gene goterms ${}".format(input_file)
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28 #cmdline_str = "touch /tmp/foo.bar"
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29 cmdline_str = self.newSplit(cmdline_str)
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30 build_ctb_run = False
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31 try:
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32 check_call(cmdline_str)
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33 build_ctb_run = True
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34 except CalledProcessError:
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35 print("Error running the build_ctb_gene goterms", file=sys.stderr)
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36 if build_ctb_run:
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37 self.copy_output_file_to_dataset()
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38 print("Building a new DB, current time: %s" % str(datetime.date.today()))
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39 print("Noe4j Database Name: http://%s:%s@%s:%s/db/data/" % (
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40 self.args.username, self.args.password, self.args.url, self.args.port))
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41 print("GFF File - Input: %s" % str(self.args.input_file))
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42
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43 def newSplit(self, value):
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44 lex = shlex.shlex(value)
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45 lex.quotes = '"'
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46 lex.whitespace_split = True
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47 lex.commenters = ''
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48 return list(lex)
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50 def copy_output_file_to_dataset(self):
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51 '''
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52 Retrieves the output files from the output directory and copies them to the Galaxy output files
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53 '''
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54 # retrieve neo4j files to the working gx directory
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55 result_file = glob.glob(self.args.mount_point + '/*')
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56 for file_name in result_file:
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57 if os.path.isfile(file_name):
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58 shutil.copy2(file_name, self.args.outputdir)
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59 elif os.path.isdir(file_name):
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60 # create the parent dir before copytree
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61 os.chdir(self.args.outputdir)
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62 shutil.copytree(file_name, file_name.rsplit('/', 1)[-1])
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63
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64 def docker_boot(self):
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65 cmd = 'docker run -d --name build_ctb_gene thoba/neo4j_galaxy_ie'
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66 check_call(cmd)
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68 def main():
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69 parser = argparse.ArgumentParser(description="Tool used to extract data about genes using locus_tags")
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70 parser.add_argument('--outputfile')
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71 parser.add_argument('--outputdir')
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72 parser.add_argument('--input_file')
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73 parser.add_argument('--mount_point')
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74 parser.add_argument('--username')
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75 parser.add_argument('--password')
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76 parser.add_argument('--url')
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77 parser.add_argument('--port')
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78 args = parser.parse_args()
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79
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80 ctb_gene_runner = BuildCtbRunner(args)
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81 ctb_gene_runner.build_ctb_gene()
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83 # boot up a neo4j docker container
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84 ctb_gene_runner.docker_boot()
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86 # docker_cmd = 'docker run '
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88 export_cmd = "export NEO4J_REST_URL=http://${args.username}:${args.password}@${args.url}:${args.port}/db/data/"
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89 try:
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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90 os.system(export_cmd)
14
4caf3e2d10e8 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 63871d62b7acd851ff2d50dc08520c17bdf834f6
sanbi-uwc
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91 except (OSError, ValueError), e:
4caf3e2d10e8 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 63871d62b7acd851ff2d50dc08520c17bdf834f6
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92 print("Error exporting the NEO4J db environmental values", e)
4
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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93
10
cb322069c7bc planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit f3af88f047a6081a46925bdbb50161ad1244b4f1
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94 # make the output directory
cb322069c7bc planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit f3af88f047a6081a46925bdbb50161ad1244b4f1
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95 if not os.path.exists(args.outputdir):
cb322069c7bc planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit f3af88f047a6081a46925bdbb50161ad1244b4f1
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96 os.makedirs(args.outputdir)
cb322069c7bc planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit f3af88f047a6081a46925bdbb50161ad1244b4f1
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97
7
d89a58d00a92 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 74c1cc58782b9960175753e731dfdd120f234b4c
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98
11
517691812452 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 3f5361a7226127ec8b8d6cb5591b5bb4f52bb6fe
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99
14
4caf3e2d10e8 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 63871d62b7acd851ff2d50dc08520c17bdf834f6
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100 if __name__ == "__main__": main()