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annotate data_manager/bowtie2_index_builder.py @ 4:d1d5feb31804 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
author iuc
date Thu, 09 May 2019 16:15:47 -0400
parents 83da94c0e4a6
children 1c0f8e9d87c6
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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_NAMES = ["bowtie2_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_bowtie2_index( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=DEFAULT_DATA_TABLE_NAMES ):
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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 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
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32 os.symlink( fasta_filename, sym_linked_fasta_filename )
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33 args = [ 'bowtie2-build', sym_linked_fasta_filename, sequence_id ]
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34 threads = os.environ.get('GALAXY_SLOTS')
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35 if threads:
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36 args.extend(['--threads', threads])
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37 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
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38 return_code = proc.wait()
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39 if return_code:
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40 print("Error building index.", file=sys.stderr)
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41 sys.exit( return_code )
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42 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=sequence_id )
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43 for data_table_name in data_table_names:
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44 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
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47 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
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48 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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49 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
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50 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
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51 return data_manager_dict
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52
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53
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54 def main():
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55 parser = optparse.OptionParser()
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56 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
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57 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
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58 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
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59 parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='append', type="string", default=None, help='data_table_name' )
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60 (options, args) = parser.parse_args()
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62 filename = args[0]
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64 params = loads( open( filename ).read() )
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65 target_directory = params[ 'output_data' ][0]['extra_files_path']
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66 os.mkdir( target_directory )
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67 data_manager_dict = {}
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69 dbkey = options.fasta_dbkey
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71 if dbkey in [ None, '', '?' ]:
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72 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
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74 sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description )
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76 # build the index
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77 build_bowtie2_index( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES )
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79 # save info to json file
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80 with open(filename, 'w') as json_out:
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81 json_out.write( dumps( data_manager_dict, sort_keys=True ) )
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84 if __name__ == "__main__":
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85 main()