Mercurial > repos > bgruening > data_manager_diamond_database_builder

changeset 5:cda0d1859f65 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Sat, 07 Feb 2015 22:35:41 -0500
parents 8bb8bec1a084
children ad69009da1b5
files data_manager/data_manager_diamond_database_builder.py
diffstat 1 files changed, 6 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_diamond_database_builder.py	Sat Feb 07 22:28:04 2015 -0500
+++ b/data_manager/data_manager_diamond_database_builder.py	Sat Feb 07 22:35:41 2015 -0500
@@ -59,7 +59,7 @@
     NCBI_DOWNLOAD_PATH = '/blast/db/FASTA/'
     COMPRESSED_EXTENSIONS = [ ( '.tar.gz', _get_stream_readers_for_tar ), ( '.tar.bz2', _get_stream_readers_for_tar ), ( '.zip', _get_stream_readers_for_zip ), ( '.fa.gz', _get_stream_readers_for_gzip ), ( '.fa.bz2', _get_stream_readers_for_bz2 ) ]
 
-    ucsc_dbkey = params['param_dict']['reference_source']['requested_dbkey'] or dbkey
+    ncbi_identifier = params['param_dict']['reference_source']['requested_identifier']
     ftp = FTP( UCSC_FTP_SERVER )
     ftp.login()
 
@@ -69,15 +69,15 @@
     get_stream_reader = None
     ext = None
     for ext, get_stream_reader in COMPRESSED_EXTENSIONS:
-        if "%s%s" % ( database_name, ext ) in path_contents:
-            ucsc_file_name = "%s%s%s" % ( UCSC_DOWNLOAD_PATH, database_name, ext )
+        if "%s%s" % ( ncbi_identifier, ext ) in path_contents:
+            ucsc_file_name = "%s%s%s" % ( UCSC_DOWNLOAD_PATH, ncbi_identifier, ext )
             break
 
     if not ucsc_file_name:
         raise Exception( 'Unable to determine filename for UCSC Genome for %s: %s' % ( ucsc_dbkey, path_contents ) )
 
     tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-ucsc-' )
-    ucsc_fasta_filename = os.path.join( tmp_dir, "%s%s" % ( database_name, ext ) )
+    ucsc_fasta_filename = os.path.join( tmp_dir, "%s%s" % ( ncbi_identifier, ext ) )
     
     fasta_base_filename = "%s.fa" % database_id
     fasta_filename = os.path.join( target_directory, fasta_base_filename )
@@ -141,8 +141,8 @@
 
 def _add_data_table_entry( data_manager_dict, data_table_entry ):
     data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
-    data_manager_dict['data_tables']['all_fasta'] = data_manager_dict['data_tables'].get( 'all_fasta', [] )
-    data_manager_dict['data_tables']['all_fasta'].append( data_table_entry )
+    data_manager_dict['data_tables']['diamond_database'] = data_manager_dict['data_tables'].get( 'diamond_database', [] )
+    data_manager_dict['data_tables']['diamond_database'].append( data_table_entry )
     return data_manager_dict