Mercurial > repos > jeremyjliu > region_motif_data_manager

comparison data_manager/data_manager_fetch_motifs.py @ 2:d5faf2b51b07 draft

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author jeremyjliu
date Sun, 11 Jan 2015 20:30:46 -0500
parents 2ed33f9b9a47
children 75d825e1b00d
comparison
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1:2ed33f9b9a47 2:d5faf2b51b07
24 24
25 url = TEST_DOWNLOAD_URL 25 url = TEST_DOWNLOAD_URL
26 fasta_reader = urllib2.urlopen( url ) 26 fasta_reader = urllib2.urlopen( url )
27 27
28 data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, params ) 28 data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, params )
29 _add_data_table_entry( data_manager_dict, data_table_entry ) 29 _add_data_table_entry( data_manager_dict, 'motif_databases', data_table_entry )
30 30
31 def _add_data_table_entry( data_manager_dict, data_table_entry ): 31 def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ):
32 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) 32 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
33 data_manager_dict['data_tables']['all_fasta'] = data_manager_dict['data_tables'].get( 'all_fasta', [] ) 33 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )
34 data_manager_dict['data_tables']['all_fasta'].append( data_table_entry ) 34 data_manager_dict['data_tables'][data_table].append( data_table_entry )
35 return data_manager_dict 35 return data_manager_dict
36 36
37 def _stream_fasta_to_file( fasta_stream, target_directory, params, close_stream=True ): 37 def _stream_fasta_to_file( fasta_stream, target_directory, params, close_stream=True ):
38 fasta_base_filename = "pouya_test_motifs.bed.bgz" 38 fasta_base_filename = "pouya_test_motifs.bed.bgz"
39 fasta_filename = os.path.join( target_directory, fasta_base_filename ) 39 fasta_filename = os.path.join( target_directory, fasta_base_filename )