Mercurial > repos > jeremyjliu > region_motif_data_manager
changeset 5:6621a6ac8bb4 draft
Uploaded
| author | jeremyjliu |
|---|---|
| date | Wed, 28 Jan 2015 22:49:33 -0500 |
| parents | 75d825e1b00d |
| children | aa0d1b185070 |
| files | data_manager/data_manager_fetch_motifs.py |
| diffstat | 1 files changed, 4 insertions(+), 5 deletions(-) [+] |
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--- a/data_manager/data_manager_fetch_motifs.py Wed Jan 28 22:39:46 2015 -0500 +++ b/data_manager/data_manager_fetch_motifs.py Wed Jan 28 22:49:33 2015 -0500 @@ -30,12 +30,12 @@ bgz_reader = urllib2.urlopen( TEST_BGZ_URL ) bgz_data_table_entry = _stream_fasta_to_file( bgz_reader, target_directory, params, - "test_bgz", "pouya_test_motifs.bed.bgz" ) + "pouya_test_motifs.bed.bgz", "test_bgz", "Test Pouya Subset BGZ (hg19)" ) _add_data_table_entry( data_manager_dict, 'motif_databases', bgz_data_table_entry ) tbi_reader = urllib2.urlopen( TEST_TBI_URL ) tbi_data_table_entry = _stream_fasta_to_file( tbi_reader, target_directory, params, - "test_tbi", "pouya_test_motifs.bed.bgz" ) + "pouya_test_motifs.bed.bgz.tbi", "test_tbi", "Test Pouya Subset TBI (hg19)" ) _add_data_table_entry( data_manager_dict, 'motif_databases', tbi_data_table_entry ) def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ): @@ -44,9 +44,8 @@ data_manager_dict['data_tables'][data_table].append( data_table_entry ) return data_manager_dict -def _stream_fasta_to_file( fasta_stream, target_directory, params, close_stream=True, - fasta_base_filename, value, name ): - fasta_base_filename = "pouya_test_motifs.bed.bgz" +def _stream_fasta_to_file( fasta_stream, target_directory, params, + fasta_base_filename, value, name, close_stream=True ): fasta_filename = os.path.join( target_directory, fasta_base_filename ) fasta_writer = open( fasta_filename, 'wb+' )