Mercurial > repos > sanbi-uwc > build_ctb_gene

annotate build_ctb_gene.py @ 8:56555326a056 draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 333add5fa185ac676c1a09b9b62e4d6c07b3bafa
author sanbi-uwc
date Mon, 16 May 2016 05:32:38 -0400
parents d89a58d00a92
children 9cc174f0fb9f
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714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
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1 #!/usr/bin/env python
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
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2 from __future__ import print_function
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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3 import argparse
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
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4 import os
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
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5 import sys
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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6 import glob
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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8 import logging
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d89a58d00a92 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 74c1cc58782b9960175753e731dfdd120f234b4c
sanbi-uwc
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d89a58d00a92 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 74c1cc58782b9960175753e731dfdd120f234b4c
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10 log = logging.getLogger(__name__)
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714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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11
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d89a58d00a92 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 74c1cc58782b9960175753e731dfdd120f234b4c
sanbi-uwc
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13 def build_ctb_gene(output_file1, output_dir, input_file, mount_point):
d89a58d00a92 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 74c1cc58782b9960175753e731dfdd120f234b4c
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14 # cmdline_str = "build_ctb_gene goterms ${}".format(input_file)
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714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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15 cmdline_str = "echo goterms"
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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16 build_ctb = False
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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17 try:
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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18 os.system(cmdline_str)
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
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19 build_ctb = True
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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20 except:
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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21 log.debug("Error running the build_ctb_gene goterms", file=sys.stderr)
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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23 # Read the files at the mount point and load the html file
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d89a58d00a92 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 74c1cc58782b9960175753e731dfdd120f234b4c
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24 if build_ctb:
d89a58d00a92 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 74c1cc58782b9960175753e731dfdd120f234b4c
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25 files = glob.glob(mount_point)
d89a58d00a92 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 74c1cc58782b9960175753e731dfdd120f234b4c
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26 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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714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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27 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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28 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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29 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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30 <title></title>
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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31 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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32 </head>
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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33 <body>
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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34 <div class="toolFormBody">
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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35 <table>
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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36 <th>Files</th>
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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37 """
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d89a58d00a92 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 74c1cc58782b9960175753e731dfdd120f234b4c
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38 for f in files:
d89a58d00a92 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 74c1cc58782b9960175753e731dfdd120f234b4c
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39 output_file1 += "<tr><td>" + f + "</td></tr>"
d89a58d00a92 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 74c1cc58782b9960175753e731dfdd120f234b4c
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40 output_file1 += """</table></div></body></html>\n"""
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714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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43 def main():
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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44 parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool")
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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45 parser.add_argument('output_file1')
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56555326a056 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 333add5fa185ac676c1a09b9b62e4d6c07b3bafa
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46 parser.add_argument('--outputdir')
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714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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47 parser.add_argument('--input_file')
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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48 parser.add_argument('--mount_point')
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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49 parser.add_argument('--username')
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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50 parser.add_argument('--password')
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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51 parser.add_argument('--url')
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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52 parser.add_argument('--port')
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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53 args = parser.parse_args()
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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54
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6098213127d7 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 225901c2aced445746de69c7e8733cfa59681869
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55 export_cmd = "export NEO4J_REST_URL=http://${args.username}:${args.password}@${args.url}:${args.port}/db/data/"
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714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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56 try:
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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57 os.system(export_cmd)
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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58 except:
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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59 log.debug("Error exporting the NEO4J db environmental values")
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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56555326a056 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 333add5fa185ac676c1a09b9b62e4d6c07b3bafa
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61 build_ctb_gene(args.output_file1, args.outputdir, args.input_file, args.mount_point)
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714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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62
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63
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714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
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64 if __name__ == "__main__": main()