Mercurial > repos > sanbi-uwc > build_ctb_gene

annotate build_ctb_gene.py @ 12:7d49ea27d9f6 draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 9ba2424793e47546990c750ac5f1129bd1e3a77c
author sanbi-uwc
date Tue, 17 May 2016 04:39:41 -0400
parents 517691812452
children 3ef417806df9
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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):
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28 #cmdline_str = "build_ctb_gene goterms ${}".format(input_file)
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29 #cmdline_str = "build_ctb_gene goterms --help"
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30 cmdline_str = "touch /tmp/foo.bar >> %s" %self.args.outputdir
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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 except CalledProcessError:
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35 print("Error running the build_ctb_gene gotermS", file=sys.stderr)
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37 self.copy_output_file_to_dataset()
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38 self.args.output_file1 = self.args.outputdir
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39
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40 def newSplit(self, value):
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41 lex = shlex.shlex(value)
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42 lex.quotes = '"'
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43 lex.whitespace_split = True
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44 lex.commenters = ''
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45 return list(lex)
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47 def copy_output_file_to_dataset(self):
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48 '''
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49 Retrieves the output files from the output directory and copies them to the Galaxy output files
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50 '''
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52 # retrieve neo4j files to the working gx directory
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53 result_file = glob.glob(self.args.mount_point + '/*')
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54 for file_name in result_file:
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55 shutil.copy(file_name, self.args.outputdir)
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57 #with open(result_file[0], 'rb') as fsrc:
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58 #with open(self.args.outputdir, 'wb') as fdest:
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59 #shutil.copy(fsrc, self.args.outputdir)
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62 def main():
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63 parser = argparse.ArgumentParser(description="Tool used to extract data about genes using locus_tags")
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64 parser.add_argument('output_file1')
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65 parser.add_argument('--outputdir')
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66 parser.add_argument('--input_file')
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67 parser.add_argument('--mount_point')
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68 parser.add_argument('--username')
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69 parser.add_argument('--password')
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70 parser.add_argument('--url')
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71 parser.add_argument('--port')
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72 args = parser.parse_args()
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74 export_cmd = "export NEO4J_REST_URL=http://${args.username}:${args.password}@${args.url}:${args.port}/db/data/"
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75 try:
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76 os.system(export_cmd)
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77 except:
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78 log.debug("Error exporting the NEO4J db environmental values")
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80 # make the output directory
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81 if not os.path.exists(args.outputdir):
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82 os.makedirs(args.outputdir)
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84 ctb_gene_runner = BuildCtbRunner(args)
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85 ctb_gene_runner.build_ctb_gene()
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87 if __name__ == "__main__": main()
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