Mercurial > repos > iuc > data_manager_bowtie_index_builder

annotate data_manager/bowtie_index_builder.py @ 4:86e9af693a33 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
author iuc
date Fri, 09 Jun 2017 06:12:02 -0400
parents ea5faedd0795
children 08a3583826fa
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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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3
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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
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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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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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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 ):
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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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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32 fasta_base_name = os.path.split( fasta_filename )[-1]
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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33 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_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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34 os.symlink( fasta_filename, sym_linked_fasta_filename )
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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35 args = [ 'bowtie-build' ]
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' )
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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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38 args.append( sym_linked_fasta_filename)
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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39 args.append( fasta_base_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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40 args.append( sym_linked_fasta_filename )
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41 tmp_stderr = tempfile.NamedTemporaryFile( prefix="tmp-data-manager-bowtie-index-builder-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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42 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
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:
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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49 chunk = tmp_stderr.read( CHUNK_SIZE )
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 )
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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53 sys.exit( 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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54 tmp_stderr.close()
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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55 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_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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56 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
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 ):
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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60 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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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61 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_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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62 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
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()
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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68 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
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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69 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='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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70 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='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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71 parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_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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72 parser.add_option( '-c', '--color_space', dest='color_space', action='store_true', default=False, help='color_space' )
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]
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77 params = json.loads( open( filename ).read() )
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78 target_directory = params[ 'output_data' ][0]['extra_files_path']
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79 os.mkdir( target_directory )
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80 data_manager_dict = {}
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81
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82 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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83
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84 if dbkey in [ None, '', '?' ]:
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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85 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( 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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86
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 sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.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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88
1
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89 # build the index
0
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90 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 )
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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91
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92 # save info to json file
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 open( filename, 'wb' ).write( json.dumps( data_manager_dict ) )
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94
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95
0
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96 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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97 main()