Mercurial > repos > iuc > data_manager_sailfish_index_builder
annotate data_manager/bwa_index_builder.py @ 0:eae04baa35a6 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
author | iuc |
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date | Tue, 05 Jan 2016 12:58:16 -0500 |
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0
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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1 #!/usr/bin/env python |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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2 #Dan Blankenberg |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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3 |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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4 import sys |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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5 import os |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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6 import tempfile |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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7 import optparse |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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8 import subprocess |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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9 |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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10 from galaxy.util.json import from_json_string, to_json_string |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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11 |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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12 |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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13 CHUNK_SIZE = 2**20 |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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14 ONE_GB = 2**30 |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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15 |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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16 DEFAULT_DATA_TABLE_NAME = "sailfish_indexes" |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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17 |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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18 def get_id_name( params, dbkey, fasta_description=None): |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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19 #TODO: ensure sequence_id is unique and does not already appear in location file |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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20 sequence_id = params['param_dict']['sequence_id'] |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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21 if not sequence_id: |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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22 sequence_id = dbkey |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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23 |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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24 sequence_name = params['param_dict']['sequence_name'] |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
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25 if not sequence_name: |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
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26 sequence_name = fasta_description |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
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27 if not sequence_name: |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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28 sequence_name = dbkey |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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29 return sequence_id, sequence_name |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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30 |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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31 def build_bwa_index( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME, color_space = False ): |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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32 #TODO: allow multiple FASTA input files |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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33 #tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-bwa-index-builder-' ) |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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34 fasta_base_name = os.path.split( fasta_filename )[-1] |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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35 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name ) |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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36 os.symlink( fasta_filename, sym_linked_fasta_filename ) |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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37 if params['param_dict']['index_algorithm'] == 'automatic': |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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38 if os.stat( fasta_filename ).st_size <= ONE_GB: #use 1 GB as cut off for memory vs. max of 2gb database size; this is somewhat arbitrary |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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39 index_algorithm = 'is' |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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40 else: |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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41 index_algorithm = 'bwtsw' |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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42 else: |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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43 index_algorithm = params['param_dict']['index_algorithm'] |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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44 |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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45 args = [ 'bwa', 'index', '-a', index_algorithm ] |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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46 if color_space: |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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47 args.append( '-c' ) |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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48 args.append( sym_linked_fasta_filename ) |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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49 tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-bwa-index-builder-stderr" ) |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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50 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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51 return_code = proc.wait() |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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52 if return_code: |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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53 tmp_stderr.flush() |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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54 tmp_stderr.seek(0) |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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55 print >> sys.stderr, "Error building index:" |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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56 while True: |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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57 chunk = tmp_stderr.read( CHUNK_SIZE ) |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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58 if not chunk: |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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59 break |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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60 sys.stderr.write( chunk ) |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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61 sys.exit( return_code ) |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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62 tmp_stderr.close() |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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63 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name ) |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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64 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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65 |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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66 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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67 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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68 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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69 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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70 return data_manager_dict |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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71 |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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72 def main(): |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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73 #Parse Command Line |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
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74 parser = optparse.OptionParser() |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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75 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' ) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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76 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' ) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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77 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' ) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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78 parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' ) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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79 parser.add_option( '-c', '--color_space', dest='color_space', action='store_true', default=False, help='color_space' ) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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80 (options, args) = parser.parse_args() |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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81 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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82 filename = args[0] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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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_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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84 params = from_json_string( open( filename ).read() ) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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85 target_directory = params[ 'output_data' ][0]['extra_files_path'] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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86 os.mkdir( target_directory ) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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87 data_manager_dict = {} |
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88 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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89 dbkey = options.fasta_dbkey |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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90 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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91 if dbkey in [ None, '', '?' ]: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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92 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) ) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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93 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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94 sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description ) |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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95 |
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96 #build the index |
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97 build_bwa_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 ) |
eae04baa35a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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98 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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99 #save info to json file |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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100 open( filename, 'wb' ).write( to_json_string( data_manager_dict ) ) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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101 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
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102 if __name__ == "__main__": main() |