Mercurial > repos > jeremyjliu > region_motif_data_manager

comparison data_manager/data_manager_fetch_motifs.py @ 5:6621a6ac8bb4 draft

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author jeremyjliu
date Wed, 28 Jan 2015 22:49:33 -0500
parents 75d825e1b00d
children aa0d1b185070
comparison
equal deleted inserted replaced
4:75d825e1b00d 5:6621a6ac8bb4
28 MM9_BGZ_URL = '' 28 MM9_BGZ_URL = ''
29 MM9_TBI_URL = '' 29 MM9_TBI_URL = ''
30 30
31 bgz_reader = urllib2.urlopen( TEST_BGZ_URL ) 31 bgz_reader = urllib2.urlopen( TEST_BGZ_URL )
32 bgz_data_table_entry = _stream_fasta_to_file( bgz_reader, target_directory, params, 32 bgz_data_table_entry = _stream_fasta_to_file( bgz_reader, target_directory, params,
33 "test_bgz", "pouya_test_motifs.bed.bgz" ) 33 "pouya_test_motifs.bed.bgz", "test_bgz", "Test Pouya Subset BGZ (hg19)" )
34 _add_data_table_entry( data_manager_dict, 'motif_databases', bgz_data_table_entry ) 34 _add_data_table_entry( data_manager_dict, 'motif_databases', bgz_data_table_entry )
35 35
36 tbi_reader = urllib2.urlopen( TEST_TBI_URL ) 36 tbi_reader = urllib2.urlopen( TEST_TBI_URL )
37 tbi_data_table_entry = _stream_fasta_to_file( tbi_reader, target_directory, params, 37 tbi_data_table_entry = _stream_fasta_to_file( tbi_reader, target_directory, params,
38 "test_tbi", "pouya_test_motifs.bed.bgz" ) 38 "pouya_test_motifs.bed.bgz.tbi", "test_tbi", "Test Pouya Subset TBI (hg19)" )
39 _add_data_table_entry( data_manager_dict, 'motif_databases', tbi_data_table_entry ) 39 _add_data_table_entry( data_manager_dict, 'motif_databases', tbi_data_table_entry )
40 40
41 def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ): 41 def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ):
42 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) 42 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
43 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] ) 43 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )
44 data_manager_dict['data_tables'][data_table].append( data_table_entry ) 44 data_manager_dict['data_tables'][data_table].append( data_table_entry )
45 return data_manager_dict 45 return data_manager_dict
46 46
47 def _stream_fasta_to_file( fasta_stream, target_directory, params, close_stream=True, 47 def _stream_fasta_to_file( fasta_stream, target_directory, params,
48 fasta_base_filename, value, name ): 48 fasta_base_filename, value, name, close_stream=True ):
49 fasta_base_filename = "pouya_test_motifs.bed.bgz"
50 fasta_filename = os.path.join( target_directory, fasta_base_filename ) 49 fasta_filename = os.path.join( target_directory, fasta_base_filename )
51 fasta_writer = open( fasta_filename, 'wb+' ) 50 fasta_writer = open( fasta_filename, 'wb+' )
52 51
53 while True: 52 while True:
54 buffer = fasta_stream.read(CHUNK_SIZE) 53 buffer = fasta_stream.read(CHUNK_SIZE)