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annotate data_manager/picard_index_builder.py @ 2:b99040168706 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 59ee07d9786f1a090053b4a13192247872389d61
author iuc
date Mon, 10 Apr 2017 06:06:23 -0400
parents dc28cd6a1d44
children ae080ff506fd
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1 #!/usr/bin/env python
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2 # Dan Blankenberg
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3 from __future__ import print_function
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5 import optparse
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6 import os
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7 import subprocess
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8 import sys
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9 from json import dumps, loads
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11 DEFAULT_DATA_TABLE_NAME = "picard_indexes"
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14 def get_id_name( params, dbkey, fasta_description=None):
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15 # TODO: ensure sequence_id is unique and does not already appear in location file
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16 sequence_id = params['param_dict']['sequence_id']
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17 if not sequence_id:
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18 sequence_id = dbkey
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20 sequence_name = params['param_dict']['sequence_name']
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21 if not sequence_name:
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22 sequence_name = fasta_description
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23 if not sequence_name:
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24 sequence_name = dbkey
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25 return sequence_id, sequence_name
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28 def build_picard_index( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ):
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29 # TODO: allow multiple FASTA input files
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30 fasta_base_name = os.path.split( fasta_filename )[-1]
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31 prefix = os.path.splitext( fasta_base_name )[0]
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32 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
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33 os.symlink( fasta_filename, sym_linked_fasta_filename )
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34 args = [ 'picard', 'CreateSequenceDictionary', 'R=%s' % sym_linked_fasta_filename, 'O=%s.dict' % prefix ]
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35 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
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36 return_code = proc.wait()
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37 if return_code:
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dc28cd6a1d44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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38 print("Error building index.", file=sys.stderr)
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39 sys.exit( return_code )
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40 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name )
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41 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
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43
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44 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
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45 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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46 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
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47 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
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48 return data_manager_dict
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49
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51 def main():
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52 parser = optparse.OptionParser()
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53 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
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54 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
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55 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
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56 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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57 (options, args) = parser.parse_args()
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59 filename = args[0]
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60
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61 params = loads( open( filename ).read() )
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62 target_directory = params[ 'output_data' ][0]['extra_files_path']
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63 os.mkdir( target_directory )
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64 data_manager_dict = {}
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65
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66 dbkey = options.fasta_dbkey
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68 if dbkey in [ None, '', '?' ]:
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69 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
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71 sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description )
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73 # build the index
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74 build_picard_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 )
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76 # save info to json file
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77 open( filename, 'wb' ).write( dumps( data_manager_dict ) )
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80 if __name__ == "__main__":
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81 main()