diff data_manager/data_manager_snpEff_download.py @ 7:a6400027d849 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 9d2052269bfbca81a5f9cd10c3153e611358a329

--- a/data_manager/data_manager_snpEff_download.py	Tue Apr 18 12:56:13 2017 -0400
+++ b/data_manager/data_manager_snpEff_download.py	Tue Oct 24 07:27:38 2017 -0400
@@ -93,8 +93,6 @@
         sys.exit( return_code )
     # search data_dir/genome_version for files
     regulation_pattern = 'regulation_(.+).bin'
-    #  annotation files that are included in SnpEff by a flag
-    annotations_dict = {'nextProt.bin': '-nextprot', 'motif.bin': '-motif', 'interactions.bin': '-interaction'}
     genome_path = os.path.join(data_dir, genome_version)
     snpeff_version = getSnpeffVersion()
     key = snpeff_version + '_' + genome_version
@@ -112,11 +110,6 @@
                         name = m.groups()[0]
                         data_table_entry = dict(key=key, version=snpeff_version, genome=genome_version, value=name, name=name)
                         _add_data_table_entry( data_manager_dict, 'snpeffv_regulationdb', data_table_entry )
-                    elif fname in annotations_dict:
-                        value = annotations_dict[fname]
-                        name = value.lstrip('-')
-                        data_table_entry = dict(key=key, version=snpeff_version, genome=genome_version, value=value, name=name)
-                        _add_data_table_entry( data_manager_dict, 'snpeffv_annotations', data_table_entry )
     return data_manager_dict