Mercurial > repos > iuc > data_manager_hisat2_index_builder

annotate data_manager/hisat2_index_builder.py @ 4:a9a26db6a455 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 17:51:36 -0400
parents e8239a46a579
children 721a2a97f31b
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1 #!/usr/bin/env python
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2 # Based heavily on the Bowtie 2 data manager wrapper script by Dan Blankenberg
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3 from __future__ import print_function
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5 import argparse
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6 import os
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7 import shlex
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8 import subprocess
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9 import sys
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10 from json import dumps, loads
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12 DEFAULT_DATA_TABLE_NAME = "hisat2_indexes"
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15 def get_id_name( params, dbkey, fasta_description=None):
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16 # TODO: ensure sequence_id is unique and does not already appear in location file
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17 sequence_id = params['param_dict']['sequence_id']
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18 if not sequence_id:
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19 sequence_id = dbkey
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21 sequence_name = params['param_dict']['sequence_name']
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22 if not sequence_name:
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23 sequence_name = fasta_description
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24 if not sequence_name:
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25 sequence_name = dbkey
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26 return sequence_id, sequence_name
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29 def build_hisat_index( data_manager_dict, options, params, sequence_id, sequence_name ):
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30 data_table_name = options.data_table_name or DEFAULT_DATA_TABLE_NAME
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31 target_directory = params[ 'output_data' ][0]['extra_files_path']
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32 if not os.path.exists( target_directory ):
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33 os.mkdir( target_directory )
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34 fasta_base_name = os.path.split( options.fasta_filename )[-1]
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35 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
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36 os.symlink( options.fasta_filename, sym_linked_fasta_filename )
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37 args = [ 'hisat2-build' ]
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38 args.extend( shlex.split( options.indexer_options ) )
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39 args.extend( [ sym_linked_fasta_filename, sequence_id ] )
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40 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
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41 return_code = proc.wait()
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42 if return_code:
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43 print("Error building index.", file=sys.stderr)
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44 sys.exit( return_code )
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45 data_table_entry = dict( value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id )
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46 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
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49 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
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50 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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51 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
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52 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
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53 return data_manager_dict
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56 def main():
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57 # Parse Command Line
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58 parser = argparse.ArgumentParser()
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59 parser.add_argument( '--output', dest='output', action='store', type=str, default=None )
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60 parser.add_argument( '--fasta_filename', dest='fasta_filename', action='store', type=str, default=None )
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61 parser.add_argument( '--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None )
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62 parser.add_argument( '--fasta_description', dest='fasta_description', action='store', type=str, default=None )
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63 parser.add_argument( '--data_table_name', dest='data_table_name', action='store', type=str, default='hisat2_indexes' )
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64 parser.add_argument( '--indexer_options', dest='indexer_options', action='store', type=str, default='' )
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65 options = parser.parse_args()
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67 filename = options.output
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69 params = loads( open( filename ).read() )
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70 data_manager_dict = {}
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72 if options.fasta_dbkey in [ None, '', '?' ]:
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73 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) )
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75 sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description )
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8dbde949a86d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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77 # build the index
8dbde949a86d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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78 build_hisat_index( data_manager_dict, options, params, sequence_id, sequence_name )
8dbde949a86d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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8dbde949a86d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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80 # save info to json file
4
a9a26db6a455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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81 open( filename, 'w' ).write( dumps( data_manager_dict ) )
a9a26db6a455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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82
0
8dbde949a86d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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83
8dbde949a86d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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84 if __name__ == "__main__":
8dbde949a86d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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85 main()