Mercurial > repos > jeremyjliu > region_motif_data_manager

comparison data_manager/data_manager_fetch_motifs.py @ 6:aa0d1b185070 draft

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author jeremyjliu
date Wed, 28 Jan 2015 23:39:30 -0500
parents 6621a6ac8bb4
children b4c2836d2e4e
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5:6621a6ac8bb4 6:aa0d1b185070
17 from galaxy.util.json import from_json_string, to_json_string 17 from galaxy.util.json import from_json_string, to_json_string
18 18
19 CHUNK_SIZE = 2**20 #1mb 19 CHUNK_SIZE = 2**20 #1mb
20 20
21 def download_motif_databases( data_manager_dict, params, target_directory, motif_db ): 21 def download_motif_databases( data_manager_dict, params, target_directory, motif_db ):
22 TEST_BGZ_URL = 'http://gehlenborg.com/wp-content/uploads/motif/pouya_test_motifs.bed.bgz'
23 TEST_TBI_URL = 'http://gehlenborg.com/wp-content/uploads/motif/pouya_test_motifs.bed.bgz.tbi'
24 POUYA_BGZ_URL = ''
25 POUYA_TBI_URL = ''
26 JOLMA_BGZ_URL = ''
27 JOLMA_TBI_URL = ''
28 MM9_BGZ_URL = ''
29 MM9_TBI_URL = ''
30 22
31 bgz_reader = urllib2.urlopen( TEST_BGZ_URL ) 23 if motif_db == "pouya":
24 BGZ = ['COMPBIO URL HERE',
25 "pouya_motifs.bed.bgz", "pouya_bgz", "Pouya Encode Motifs (hg19) BGZ"]
26 TBI = ['COMPBIO URL HERE',
27 "pouya_motifs.bed.bgz.tbi", "pouya_tbi", "Pouya Encode Motifs (hg19) TBI"]
28 elif motif_db == "jaspar":
29 BGZ = ['COMPBIO URL HERE',
30 "jaspar_jolma_motifs.bed.bgz", "jaspar_bgz", "Jaspar and Jolma Motifs (hg19) BGZ"]
31 TBI = ['COMPBIO URL HERE',
32 "jaspar_jolma_motifs.bed.bgz.tbi", "jaspar_tbi", "Jaspar and Jolma Motifs (hg19) TBI"]
33 elif motif_db == "mouse":
34 BGZ = ['COMPBIO URL HERE',
35 "mouse_motifs.bed.bgz", "mouse_bgz", "Mouse Motifs (mm9) BGZ"]
36 TBI = ['COMPBIO URL HERE',
37 "mouse_motifs.bed.bgz.tbi", "mouse_tbi", "Mouse Motifs (mm9) TBI"]
38 else:
39 BGZ = ['http://gehlenborg.com/wp-content/uploads/motif/pouya_test_motifs.bed.bgz',
40 "pouya_test_motifs.bed.bgz", "test_bgz", "Test Pouya Subset (hg19) BGZ"]
41 TBI = ['http://gehlenborg.com/wp-content/uploads/motif/pouya_test_motifs.bed.bgz.tbi',
42 "pouya_test_motifs.bed.bgz.tbi", "test_tbi", "Test Pouya Subset (hg19) TBI"]
43
44 bgz_reader = urllib2.urlopen( BGZ[0] )
32 bgz_data_table_entry = _stream_fasta_to_file( bgz_reader, target_directory, params, 45 bgz_data_table_entry = _stream_fasta_to_file( bgz_reader, target_directory, params,
33 "pouya_test_motifs.bed.bgz", "test_bgz", "Test Pouya Subset BGZ (hg19)" ) 46 BGZ[1], BGZ[2], BGZ[3] )
34 _add_data_table_entry( data_manager_dict, 'motif_databases', bgz_data_table_entry ) 47 _add_data_table_entry( data_manager_dict, 'motif_databases', bgz_data_table_entry )
35 48
36 tbi_reader = urllib2.urlopen( TEST_TBI_URL ) 49 tbi_reader = urllib2.urlopen( TBI[0] )
37 tbi_data_table_entry = _stream_fasta_to_file( tbi_reader, target_directory, params, 50 tbi_data_table_entry = _stream_fasta_to_file( tbi_reader, target_directory, params,
38 "pouya_test_motifs.bed.bgz.tbi", "test_tbi", "Test Pouya Subset TBI (hg19)" ) 51 TBI[1], TBI[2], TBI[3] )
39 _add_data_table_entry( data_manager_dict, 'motif_databases', tbi_data_table_entry ) 52 _add_data_table_entry( data_manager_dict, 'motif_databases', tbi_data_table_entry )
40 53
41 def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ): 54 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', {} ) 55 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, [] ) 56 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )