Mercurial > repos > jeremyjliu > region_motif_data_manager
changeset 4:75d825e1b00d draft
Uploaded
| author | jeremyjliu |
|---|---|
| date | Wed, 28 Jan 2015 22:39:46 -0500 |
| parents | 8bf194e522bf |
| children | 6621a6ac8bb4 |
| files | data_manager/data_manager_fetch_motifs.py tool-data/motif_databases.loc.sample |
| diffstat | 2 files changed, 21 insertions(+), 12 deletions(-) [+] |
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--- a/data_manager/data_manager_fetch_motifs.py Sun Jan 11 20:40:09 2015 -0500 +++ b/data_manager/data_manager_fetch_motifs.py Wed Jan 28 22:39:46 2015 -0500 @@ -19,14 +19,24 @@ CHUNK_SIZE = 2**20 #1mb def download_motif_databases( data_manager_dict, params, target_directory, motif_db ): - TEST_DOWNLOAD_URL = 'http://gehlenborg.com/wp-content/uploads/motif/pouya_test_motifs.bed.bgz' - #TO DO: Add tbi file + TEST_BGZ_URL = 'http://gehlenborg.com/wp-content/uploads/motif/pouya_test_motifs.bed.bgz' + TEST_TBI_URL = 'http://gehlenborg.com/wp-content/uploads/motif/pouya_test_motifs.bed.bgz.tbi' + POUYA_BGZ_URL = '' + POUYA_TBI_URL = '' + JOLMA_BGZ_URL = '' + JOLMA_TBI_URL = '' + MM9_BGZ_URL = '' + MM9_TBI_URL = '' - url = TEST_DOWNLOAD_URL - fasta_reader = urllib2.urlopen( url ) - - data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, params ) - _add_data_table_entry( data_manager_dict, 'motif_databases', data_table_entry ) + 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" ) + _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" ) + _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 ): data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) @@ -34,7 +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 ): +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" fasta_filename = os.path.join( target_directory, fasta_base_filename ) fasta_writer = open( fasta_filename, 'wb+' ) @@ -49,7 +60,7 @@ fasta_stream.close() fasta_writer.close() - return dict( value="test", name="Test Pouya Subset (hg19)", path=fasta_base_filename ) + return dict( value=value, name=name, path=fasta_base_filename ) def main(): #Parse Command Line
--- a/tool-data/motif_databases.loc.sample Sun Jan 11 20:40:09 2015 -0500 +++ b/tool-data/motif_databases.loc.sample Wed Jan 28 22:39:46 2015 -0500 @@ -1,9 +1,7 @@ # #<value> <display_name> <file_path> # -#So, all_fasta.loc could look something like this: +#So, motif_databases.loc could look something like this: # #test Test Pouya Subset (hg19) /<path_to_galaxy>/tool-data/motifs/pouya_test_motifs.bed.bgz -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa #