From 133825d7947a75bab6062df9c7d7d33380d64d70 Mon Sep 17 00:00:00 2001 From: Georgios Koutsovoulos Date: Wed, 5 Apr 2023 11:43:15 +0200 Subject: [PATCH] v1.0.2 Removed -target_only from blastdbcmd causing occasionally the command to end prematurely --- .gitignore | 1 + avp | 1 + depot/interface.py | 2 +- depot/prepare.py | 2 +- 4 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index 22fcb9c..966af71 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ *.pyc *.dev +.DS_Store diff --git a/avp b/avp index f44fb9b..4b01135 100755 --- a/avp +++ b/avp @@ -1,4 +1,5 @@ #!/usr/bin/env python3 +#v1.0.2 from depot.interface import main diff --git a/depot/interface.py b/depot/interface.py index abf8f03..81f7d57 100644 --- a/depot/interface.py +++ b/depot/interface.py @@ -23,7 +23,7 @@ from docopt import docopt def main(): - args = docopt(__doc__,version='1.0.1', options_first=True) + args = docopt(__doc__,version='1.0.2', options_first=True) if args[''] == 'prepare': import depot.prepare as prepare prepare.main() diff --git a/depot/prepare.py b/depot/prepare.py index 60591d1..0e0bb03 100755 --- a/depot/prepare.py +++ b/depot/prepare.py @@ -237,7 +237,7 @@ def main(): setblastlog_path = os.path.join(tmp_folder,"setblast.log") if mode == "blast": - blastdbcmd_command = 'blastdbcmd -db '+ config_opts["blast_db_path"] + ' -dbtype ' + dbtype + ' -entry_batch ' + extract_id_path + ' -target_only -outfmt ">%a@%T\n%s" -logfile ' + setblastlog_path + ' -out ' + setblastfa_path + blastdbcmd_command = 'blastdbcmd -db '+ config_opts["blast_db_path"] + ' -dbtype ' + dbtype + ' -entry_batch ' + extract_id_path + ' -outfmt ">%a@%T\n%s" -logfile ' + setblastlog_path + ' -out ' + setblastfa_path subprocess.call(blastdbcmd_command, shell= True) else: # GK This is specific to SwissProt for now, have to test for UniProt in the future if mode == "sp":