Mercurial > repos > dfornika > data_manager_build_mob_suite_database

changeset 19:6883b8116d0d draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_mob_suite_database/ commit ded3b42d8a746eac2973cc17826160e43ac11186-dirty
author dfornika
date Mon, 24 Jun 2019 15:10:19 -0400
parents bf35d745b493
children 4955ab76ccf8
files data_manager/mob_suite_build_database.py
diffstat 1 files changed, 3 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/mob_suite_build_database.py	Mon Jun 24 14:38:54 2019 -0400
+++ b/data_manager/mob_suite_build_database.py	Mon Jun 24 15:10:19 2019 -0400
@@ -45,7 +45,7 @@
 
     os.rename(
         os.path.join(target_directory, database_path, 'references_updated.fasta'),
-        os.path.join(target_directory, database_path, 'ncbi_plasmid_full_seqs.fas')
+        os.path.join(target_directory, database_path, 'plasmids.fas')
     )
 
     print("Sleeping for 20s")
@@ -53,14 +53,14 @@
     print("Sleep ending")
     
     makeblastdb_args_list = [
-        '-in', os.path.join(database_path, 'ncbi_plasmid_full_seqs.fas'),
+        '-in', os.path.join(database_path, 'plasmids.fas'),
         '-dbtype', 'nucl',
     ]
     
     subprocess.check_call(['makeblastdb'] + makeblastdb_args_list, cwd=target_directory)
 
     mash_sketch_args_list = [
-        '-i', os.path.join(database_path, 'ncbi_plasmid_full_seqs.fas'),
+        '-i', os.path.join(database_path, 'plasmids.fas'),
     ]
 
     subprocess.check_call(['mash', 'sketch'] + mash_sketch_args_list, cwd=target_directory)