Mercurial > repos > iuc > data_manager_bowtie_index_builder

annotate data_manager/bowtie_index_builder.py @ 7:39a922d01b0d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit a54e50916ebdb0858b049cdc549a43df801e1a71
author iuc
date Tue, 21 May 2024 07:35:37 +0000
parents 08a3583826fa
children
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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1 #!/usr/bin/env python
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86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
iuc
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2 from __future__ import print_function
86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
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35c1e3785c90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 596a23abc0c657eff218d16df685b427ae7cdd0a
iuc
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4 import json
35c1e3785c90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 596a23abc0c657eff218d16df685b427ae7cdd0a
iuc
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5 import optparse
35c1e3785c90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 596a23abc0c657eff218d16df685b427ae7cdd0a
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6 import os
35c1e3785c90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 596a23abc0c657eff218d16df685b427ae7cdd0a
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7 import subprocess
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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8 import sys
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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9 import tempfile
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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11 CHUNK_SIZE = 2**20
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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13 DEFAULT_DATA_TABLE_NAME = "bowtie_indexes"
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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16 def get_id_name(params, dbkey, fasta_description=None):
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17 # TODO: ensure sequence_id is unique and does not already appear in location file
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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18 sequence_id = params['param_dict']['sequence_id']
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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19 if not sequence_id:
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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20 sequence_id = dbkey
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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22 sequence_name = params['param_dict']['sequence_name']
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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23 if not sequence_name:
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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24 sequence_name = fasta_description
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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25 if not sequence_name:
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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26 sequence_name = dbkey
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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27 return sequence_id, sequence_name
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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29
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30 def build_bowtie_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME, color_space=False):
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35c1e3785c90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 596a23abc0c657eff218d16df685b427ae7cdd0a
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31 # TODO: allow multiple FASTA input files
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32 fasta_base_name = os.path.split(fasta_filename)[-1]
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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33 sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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34 os.symlink(fasta_filename, sym_linked_fasta_filename)
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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35 args = ['bowtie-build']
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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36 if color_space:
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37 args.append('-C')
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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38 args.append(sym_linked_fasta_filename)
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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39 args.append(fasta_base_name)
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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40 args.append(sym_linked_fasta_filename)
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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41 tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-bowtie-index-builder-stderr")
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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42 proc = subprocess.Popen(args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno())
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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43 return_code = proc.wait()
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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44 if return_code:
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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45 tmp_stderr.flush()
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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46 tmp_stderr.seek(0)
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86e9af693a33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
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47 print("Error building index:", file=sys.stderr)
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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48 while True:
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49 chunk = tmp_stderr.read(CHUNK_SIZE)
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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50 if not chunk:
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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51 break
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52 sys.stderr.write(chunk)
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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53 sys.exit(return_code)
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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54 tmp_stderr.close()
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55 data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name)
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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56 _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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59 def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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60 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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61 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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62 data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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63 return data_manager_dict
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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66 def main():
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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67 parser = optparse.OptionParser()
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68 parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename')
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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69 parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey')
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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70 parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description')
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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71 parser.add_option('-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name')
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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72 parser.add_option('-c', '--color_space', dest='color_space', action='store_true', default=False, help='color_space')
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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73 (options, args) = parser.parse_args()
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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74
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75 filename = args[0]
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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76
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77 with open(filename) as fh:
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78 params = json.load(fh)
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79 target_directory = params['output_data'][0]['extra_files_path']
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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80 os.mkdir(target_directory)
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81 data_manager_dict = {}
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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82
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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83 dbkey = options.fasta_dbkey
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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84
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08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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85 if dbkey in [None, '', '?']:
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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86 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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87
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08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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88 sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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89
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35c1e3785c90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 596a23abc0c657eff218d16df685b427ae7cdd0a
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90 # build the index
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08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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91 build_bowtie_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME, color_space=options.color_space)
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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92
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35c1e3785c90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 596a23abc0c657eff218d16df685b427ae7cdd0a
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93 # save info to json file
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94 with open(filename, 'w') as fh:
08a3583826fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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95 json.dump(data_manager_dict, fh, sort_keys=True)
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96
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97
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0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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98 if __name__ == "__main__":
0a0c648498e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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99 main()