Mercurial > repos > scottx611x > data_manager_fetch_gene_annotation
annotate data_manager/data_manager.py @ 47:3a02b8ab423a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
author | iuc |
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date | Sun, 22 Nov 2020 12:48:13 +0000 |
parents | 9346d2955707 |
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rev | line source |
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47
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
parents:
46
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changeset
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1 # -*- coding: utf-8 -*- |
46
9346d2955707
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
diff
changeset
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2 import argparse |
47
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
parents:
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3 import bz2 |
46
9346d2955707
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
diff
changeset
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4 import datetime |
47
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
parents:
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5 import gzip |
46
9346d2955707
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
diff
changeset
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6 import json |
9346d2955707
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
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7 import os |
47
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
parents:
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8 import shutil |
46
9346d2955707
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
diff
changeset
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9 import sys |
9346d2955707
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
diff
changeset
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10 import uuid |
47
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
parents:
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11 import zipfile |
46
9346d2955707
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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diff
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12 |
47
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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13 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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14 # Nice solution to opening compressed files (zip/bz2/gz) transparently |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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15 # https://stackoverflow.com/a/13045892/638445 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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16 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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17 class CompressedFile(object): |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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18 magic = None |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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19 file_type = None |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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20 mime_type = None |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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21 proper_extension = None |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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22 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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23 def __init__(self, f): |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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24 # f is an open file or file like object |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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25 self.f = f |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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26 self.accessor = self.open() |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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27 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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28 @classmethod |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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29 def is_magic(self, data): |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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30 return data.startswith(self.magic) |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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31 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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32 def open(self): |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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33 return None |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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34 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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35 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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36 class ZIPFile(CompressedFile): |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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37 magic = '\x50\x4b\x03\x04' |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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38 file_type = 'zip' |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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39 mime_type = 'compressed/zip' |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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40 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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41 def open(self): |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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42 return zipfile.ZipFile(self.f) |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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43 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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44 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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45 class BZ2File(CompressedFile): |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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46 magic = '\x42\x5a\x68' |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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47 file_type = 'bz2' |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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48 mime_type = 'compressed/bz2' |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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49 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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50 def open(self): |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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51 return bz2.BZ2File(self.f) |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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52 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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53 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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54 class GZFile(CompressedFile): |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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55 magic = '\x1f\x8b\x08' |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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56 file_type = 'gz' |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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57 mime_type = 'compressed/gz' |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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58 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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59 def open(self): |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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60 return gzip.GzipFile(self.f) |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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61 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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62 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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63 # factory function to create a suitable instance for accessing files |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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64 def get_compressed_file(filename): |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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65 with open(filename, 'rb') as f: |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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66 start_of_file = f.read(1024) |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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67 f.seek(0) |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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68 for cls in (ZIPFile, BZ2File, GZFile): |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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69 if cls.is_magic(start_of_file): |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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70 f.close() |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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71 return cls(filename) |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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72 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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73 return None |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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74 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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75 |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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76 try: |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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77 # For Python 3.0 and later |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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78 from urllib.request import urlretrieve |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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79 except ImportError: |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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80 # Fall back to Python 2's urllib2 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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81 from urllib import urlretrieve |
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82 |
9346d2955707
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
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83 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
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84 def url_download(url): |
9346d2955707
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
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85 """Attempt to download gene annotation file from a given url |
9346d2955707
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
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86 :param url: full url to gene annotation file |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
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87 :type url: str. |
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88 :returns: name of downloaded gene annotation file |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
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89 :raises: ContentDecodingError, IOError |
9346d2955707
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
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90 """ |
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91 |
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92 # Generate file_name |
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93 file_name = url.split('/')[-1] |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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94 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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95 try: |
3a02b8ab423a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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96 # download URL (FTP and HTTP work, probably local and data too) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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97 urlretrieve(url, file_name) |
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98 |
47
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99 # uncompress file if needed |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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100 cf = get_compressed_file(file_name) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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101 if cf is not None: |
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102 uncompressed_file_name = os.path.splitext(file_name)[0] |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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103 with open(uncompressed_file_name, 'w+') as uncompressed_file: |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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104 shutil.copyfileobj(cf.accessor, uncompressed_file) |
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105 os.remove(file_name) |
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106 file_name = uncompressed_file_name |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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107 except IOError as e: |
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108 sys.stderr.write('Error occured downloading reference file: %s' % e) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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109 os.remove(file_name) |
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110 return file_name |
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111 |
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112 |
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113 def main(): |
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114 parser = argparse.ArgumentParser(description='Create data manager JSON.') |
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115 parser.add_argument('--out', dest='output', action='store', help='JSON filename') |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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116 parser.add_argument('--name', dest='name', action='store', default=uuid.uuid4(), help='Data table entry unique ID') |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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117 parser.add_argument('--url', dest='url', action='store', help='Url to download gtf file from') |
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118 |
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119 args = parser.parse_args() |
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120 |
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121 work_dir = os.getcwd() |
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122 |
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123 # Attempt to download gene annotation file from given url |
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124 gene_annotation_file_name = url_download(args.url) |
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125 |
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126 # Update Data Manager JSON and write to file |
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127 data_manager_entry = { |
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128 'data_tables': { |
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129 'gff_gene_annotations': { |
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130 'value': str(datetime.datetime.now()), |
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131 'dbkey': str(args.name), |
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132 'name': gene_annotation_file_name, |
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133 'path': os.path.join(work_dir, gene_annotation_file_name) |
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134 } |
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135 } |
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136 } |
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137 |
47
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138 with open(os.path.join(args.output), 'w+') as fh: |
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139 json.dump(data_manager_entry, fh, sort_keys=True) |
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140 |
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141 |
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142 if __name__ == '__main__': |
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143 main() |